ClusterQB - Contribuciones del usuario [es]

Index

2022-11-28T19:15:27Z

Rbetanzos:

Contenido.

<h2> A </h2>

*[[Título de la página a visitar|Título del link]]: Comentarios
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<h2> B </h2>

*[[Título de la página a visitar|Título del link]]: Comentarios
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<h2> C </h2>

*[[Conexion cluster qb|Conexión Cluster]]: Comentarios
*[[Título de la página a visitar|Título del link]]: Comentarios

<h2> D </h2>

* [[Dinámica Molecular Proteína Solvente desde Jupyter Notebook|Dinámica Molecular]]: Corriendo una DM desde Jupyter
* [[Docking proteína-ligando|Docking molecular proteína-ligando]]: Cómo correr un docking AutoDock4 en el clúster
* [[Docking sesgado|Docking sesgado]]:Docking sesgado
* [[Docking Sesgado proteína-ligando|ADBias proteína-ligando]]: Comentarios

<h2> E </h2>

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<h2> F </h2>

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<h2> G </h2>

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<h2> H </h2>

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<h2> I </h2>

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<h2> J </h2>

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<h2> K </h2>

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<h2>L </h2>

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<h2>M </h2>

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<h2>N </h2>

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<h2>Ñ </h2>

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<h2>O </h2>

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<h2>P </h2>
* [[Prerequisitos cluster|prerequisitos para uso del Cluster]]: Sugerencia
* [[Proxy|proxy]]: Proxy

<h2>Q </h2>

*[[Título de la página a visitar|Título del link]]: Comentarios
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<h2>R </h2>
* [[Recursos|Recursos]]:

<h2>S </h2>

* [[Servidores de interés|Páginas útiles]]: Links a páginas de interes para el laboratorio
* [[Sitios de Fenoles|Sitios de fenoles]]: Sitios de Fenoles
* [[Sshkeys|SSH keys]]:

<h2>T </h2>

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<h2>U </h2>
* [[Usoslurm|Uso del Slurm]]:

<h2>V </h2>

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<h2>W</h2>

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<h2>X</h2>

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<h2>Y</h2>

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<h2>Z</h2>

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Usuario:Glyco

2022-11-28T18:52:25Z

Rbetanzos:

<h1> Rafael Betanzos San Juan</h1>

<h2> Creación de usuarios </h2>

Sitios de Fenoles

2022-11-13T18:15:34Z

Rbetanzos: /* Running sugar in the command line step by step */

=== Introduction: ===
The calculation of solvent site clusters allows to generate information related to the area, time, and type of interactions. That said, we present a brief tutorial for calculating solvent sites using the results of the molecular dynamics run with mixed solvents as input information.

{| class="wikitable" style="margin:auto"
|+ Pipeline Summary
|-
! Header Step !! Description !! Input !! Output !! Note
|-
| Reference || PDB reference provides ||
* receptor_ref.pdb
|| X ||
|-
| Dynamics|| Run molecular dynamics with phenols. ||
* receptor_ref.pdb
* receptor.nc
* receptor.prmtop
|| Trajectory, parameters and reference files.|| Save the values of trajectory time and total frames.
|-
| Phenol Sites|| Calculate phenol clusters with molecular dynamics results.||
* receptor.prmtop
* receptor.nc
* receptor_ref.pdb
* parameters.in
* run_sugar.sh
* sugar-gitlab-directory
|| Molsites, overlaps and restime.|| VMD has to be installed to run the cluster scripts.
|}

Note: It’s important to have [https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD] installed. You can download all necessary files by clicking here.

== Running sugar in the command line step by step ==

Untar the hotspots.tar.bz2 file:
yourpath:$ tar -xf hotspots.tar.bz2 -C hotspots/
You will get the following files:

# inputs/
#* 4mrhA_phe-opc_HMR-noWAT.prmtop
#* MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
#* 4mrhA_ref.pdb
#* parameters.in
#* run_sugar.sh
# outputs/
#* cd44_10_14_FEN_DU/
#* molsites/
#** SS_Res_AT.pdb
#* overlaps/
#** overlap_Res_AT.pdb
#** temp_Res_AT.pdb
#** rmsd_fit.csv
#* restime/
#** SS_#_Res_AT.site
# references/
#* 5SC5-A.pdb
# sugar_clusters_tcl/
#* main.tcl
#* overlap.tcl
#* parameters_example.in
#* parser.tcl
#* pru_main.tcl
#* qt_clustering.tcl
#* README.md
#* residence_time.tcl
#* solvent.tcl
#* sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.
FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate the cluster. Its expressed in frames per nanosecond
CLUSTER_RADIUS = 1.4 # Indicates the radius from the dummy atom center in which the phenols are found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent and cosolvent if TRUE. If FALSE only runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where the phenol is found. e.g. 0.1 = 10% of the time.

Check the path in the next files:
# /inputs/run_sugar.sh
# vmd
# hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
# Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

# Tutorial

=== Molecular dynamics ===

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

# Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP = 10 step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS = 0.6 FLOAT
BINDING_SITE = resid 44 46 48 55 57 64 67 Binding Site (atomselect vmd class)
SOLVENT = TRUE
SOLVENT_THRESHOLD = 0.1 Inferior edge for pre-clusters
COSOLVENT = ETA atomselect vmd class
CS_ATOM_PROBE = O1, H1, C1 atomselect vmd class
COSOLVENT_THRESHOLD = 0.2
N_CUT_RATIO = 0.05 porcentaje de corte para armar los precluster

Run the job

$ ./run_ugar.sh

=== Visualization and analysis. ===
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

{| Directory || File || Content || Note
|-
| Work directory || sugar.out || Info about the run ||
|-|}

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

== You will get the following files: ==
inputs/
4mrhA_phe-opc_HMR-noWAT.prmtop
MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
4mrhA_ref.pdb
parameters.in
run_sugar.sh
outputs/
cd44_10_14_FEN_DU/
molsites/
SS_Res_AT.pdb
overlaps/
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
restime/
SS_#_Res_AT.site
references/
5SC5-A.pdb
sugar_clusters_tcl/
main.tcl
overlap.tcl
parameters_example.in
parser.tcl
pru_main.tcl
qt_clustering.tcl
README.md
residence_time.tcl
solvent.tcl
sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.

FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate
the cluster. Its expressed in frames per
nanosecond
CLUSTER_RADIUS= 1.4 # Indicates the radius from the dummy
atom center in which the phenols are
found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent
and cosolvent if TRUE. If FALSE only
runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where
the phenol is found. e.g. 0.1 = 10% of
the time.

Check the path in the next files:
/inputs/run_sugar.sh
vmd
hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

Beta color code in VMD.

Highest scored site
Middle scored site
Lowest scored site

Tutorial

Molecular dynamics

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

Sitios de Fenoles

2022-11-13T18:09:55Z

Rbetanzos: /* inputs/ */

=== Introduction: ===
The calculation of solvent site clusters allows to generate information related to the area, time, and type of interactions. That said, we present a brief tutorial for calculating solvent sites using the results of the molecular dynamics run with mixed solvents as input information.

{| class="wikitable" style="margin:auto"
|+ Pipeline Summary
|-
! Header Step !! Description !! Input !! Output !! Note
|-
| Reference || PDB reference provides ||
* receptor_ref.pdb
|| X ||
|-
| Dynamics|| Run molecular dynamics with phenols. ||
* receptor_ref.pdb
* receptor.nc
* receptor.prmtop
|| Trajectory, parameters and reference files.|| Save the values of trajectory time and total frames.
|-
| Phenol Sites|| Calculate phenol clusters with molecular dynamics results.||
* receptor.prmtop
* receptor.nc
* receptor_ref.pdb
* parameters.in
* run_sugar.sh
* sugar-gitlab-directory
|| Molsites, overlaps and restime.|| VMD has to be installed to run the cluster scripts.
|}

Note: It’s important to have [https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD] installed. You can download all necessary files by clicking here.

== Running sugar in the command line step by step ==

Untar the hotspots.tar.bz2 file:

yourpath:$ tar -xf hotspots.tar.bz2 -C hotspots/

You will get the following files:

# inputs/
#* 4mrhA_phe-opc_HMR-noWAT.prmtop
#* MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
#* 4mrhA_ref.pdb
#* parameters.in
#* run_sugar.sh
# outputs/
#* cd44_10_14_FEN_DU/
#* molsites/
#** SS_Res_AT.pdb
#* overlaps/
#** overlap_Res_AT.pdb
#** temp_Res_AT.pdb
#** rmsd_fit.csv
#* restime/
#** SS_#_Res_AT.site
# references/
#* 5SC5-A.pdb
# sugar_clusters_tcl/
#* main.tcl
#* overlap.tcl
#* parameters_example.in
#* parser.tcl
#* pru_main.tcl
#* qt_clustering.tcl
#* README.md
#* residence_time.tcl
#* solvent.tcl
#* sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.
FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate the cluster. Its expressed in frames per nanosecond
CLUSTER_RADIUS = 1.4 # Indicates the radius from the dummy atom center in which the phenols are found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent and cosolvent if TRUE. If FALSE only runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where the phenol is found. e.g. 0.1 = 10% of the time.

=== Check the path in the next files: ===
# /inputs/run_sugar.sh
# vmd
# hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
# Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

# Tutorial

=== Molecular dynamics ===

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

# Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

== You will get the following files: ==
inputs/
4mrhA_phe-opc_HMR-noWAT.prmtop
MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
4mrhA_ref.pdb
parameters.in
run_sugar.sh
outputs/
cd44_10_14_FEN_DU/
molsites/
SS_Res_AT.pdb
overlaps/
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
restime/
SS_#_Res_AT.site
references/
5SC5-A.pdb
sugar_clusters_tcl/
main.tcl
overlap.tcl
parameters_example.in
parser.tcl
pru_main.tcl
qt_clustering.tcl
README.md
residence_time.tcl
solvent.tcl
sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.

FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate
the cluster. Its expressed in frames per
nanosecond
CLUSTER_RADIUS= 1.4 # Indicates the radius from the dummy
atom center in which the phenols are
found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent
and cosolvent if TRUE. If FALSE only
runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where
the phenol is found. e.g. 0.1 = 10% of
the time.

Check the path in the next files:
/inputs/run_sugar.sh
vmd
hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

Beta color code in VMD.

Highest scored site
Middle scored site
Lowest scored site

Tutorial

Molecular dynamics

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

Sitios de Fenoles

2022-11-13T18:09:19Z

Rbetanzos: /* Running sugar in the command line step by step */

=== Introduction: ===
The calculation of solvent site clusters allows to generate information related to the area, time, and type of interactions. That said, we present a brief tutorial for calculating solvent sites using the results of the molecular dynamics run with mixed solvents as input information.

{| class="wikitable" style="margin:auto"
|+ Pipeline Summary
|-
! Header Step !! Description !! Input !! Output !! Note
|-
| Reference || PDB reference provides ||
* receptor_ref.pdb
|| X ||
|-
| Dynamics|| Run molecular dynamics with phenols. ||
* receptor_ref.pdb
* receptor.nc
* receptor.prmtop
|| Trajectory, parameters and reference files.|| Save the values of trajectory time and total frames.
|-
| Phenol Sites|| Calculate phenol clusters with molecular dynamics results.||
* receptor.prmtop
* receptor.nc
* receptor_ref.pdb
* parameters.in
* run_sugar.sh
* sugar-gitlab-directory
|| Molsites, overlaps and restime.|| VMD has to be installed to run the cluster scripts.
|}

Note: It’s important to have [https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD] installed. You can download all necessary files by clicking here.

== Running sugar in the command line step by step ==

Untar the hotspots.tar.bz2 file:

yourpath:$ tar -xf hotspots.tar.bz2 -C hotspots/

You will get the following files:

=== inputs/ ===
#* 4mrhA_phe-opc_HMR-noWAT.prmtop
#* MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
#* 4mrhA_ref.pdb
#* parameters.in
#* run_sugar.sh
# outputs/
#* cd44_10_14_FEN_DU/
#* molsites/
#** SS_Res_AT.pdb
#* overlaps/
#** overlap_Res_AT.pdb
#** temp_Res_AT.pdb
#** rmsd_fit.csv
#* restime/
#** SS_#_Res_AT.site
# references/
#* 5SC5-A.pdb
# sugar_clusters_tcl/
#* main.tcl
#* overlap.tcl
#* parameters_example.in
#* parser.tcl
#* pru_main.tcl
#* qt_clustering.tcl
#* README.md
#* residence_time.tcl
#* solvent.tcl
#* sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.
FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate the cluster. Its expressed in frames per nanosecond
CLUSTER_RADIUS = 1.4 # Indicates the radius from the dummy atom center in which the phenols are found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent and cosolvent if TRUE. If FALSE only runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where the phenol is found. e.g. 0.1 = 10% of the time.

=== Check the path in the next files: ===
# /inputs/run_sugar.sh
# vmd
# hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
# Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

# Tutorial

=== Molecular dynamics ===

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

# Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

== You will get the following files: ==
inputs/
4mrhA_phe-opc_HMR-noWAT.prmtop
MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
4mrhA_ref.pdb
parameters.in
run_sugar.sh
outputs/
cd44_10_14_FEN_DU/
molsites/
SS_Res_AT.pdb
overlaps/
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
restime/
SS_#_Res_AT.site
references/
5SC5-A.pdb
sugar_clusters_tcl/
main.tcl
overlap.tcl
parameters_example.in
parser.tcl
pru_main.tcl
qt_clustering.tcl
README.md
residence_time.tcl
solvent.tcl
sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.

FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate
the cluster. Its expressed in frames per
nanosecond
CLUSTER_RADIUS= 1.4 # Indicates the radius from the dummy
atom center in which the phenols are
found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent
and cosolvent if TRUE. If FALSE only
runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where
the phenol is found. e.g. 0.1 = 10% of
the time.

Check the path in the next files:
/inputs/run_sugar.sh
vmd
hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

Beta color code in VMD.

Highest scored site
Middle scored site
Lowest scored site

Tutorial

Molecular dynamics

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

Sitios de Fenoles

2022-11-13T17:49:23Z

Rbetanzos: /* Introduction: */

=== Introduction: ===
The calculation of solvent site clusters allows to generate information related to the area, time, and type of interactions. That said, we present a brief tutorial for calculating solvent sites using the results of the molecular dynamics run with mixed solvents as input information.

{| class="wikitable" style="margin:auto"
|+ Pipeline Summary
|-
! Header Step !! Description !! Input !! Output !! Note
|-
| Reference || PDB reference provides ||
* receptor_ref.pdb
|| X ||
|-
| Dynamics|| Run molecular dynamics with phenols. ||
* receptor_ref.pdb
* receptor.nc
* receptor.prmtop
|| Trajectory, parameters and reference files.|| Save the values of trajectory time and total frames.
|-
| Phenol Sites|| Calculate phenol clusters with molecular dynamics results.||
* receptor.prmtop
* receptor.nc
* receptor_ref.pdb
* parameters.in
* run_sugar.sh
* sugar-gitlab-directory
|| Molsites, overlaps and restime.|| VMD has to be installed to run the cluster scripts.
|}

Note: It’s important to have [https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD] installed. You can download all necessary files by clicking here.

== Running sugar in the command line step by step ==

Untar the hotspots.tar.bz2 file:

yourpath:$ tar -xf hotspots.tar.bz2 -C hotspots/

You will get the following files:
inputs/
4mrhA_phe-opc_HMR-noWAT.prmtop
MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
4mrhA_ref.pdb
parameters.in
run_sugar.sh
outputs/
cd44_10_14_FEN_DU/
molsites/
SS_Res_AT.pdb
overlaps/
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
restime/
SS_#_Res_AT.site
references/
5SC5-A.pdb
sugar_clusters_tcl/
main.tcl
overlap.tcl
parameters_example.in
parser.tcl
pru_main.tcl
qt_clustering.tcl
README.md
residence_time.tcl
solvent.tcl
sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.
FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate
the cluster. Its expressed in frames per
nanosecond
CLUSTER_RADIUS= 1.4 # Indicates the radius from the dummy
atom center in which the phenols are
found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent
and cosolvent if TRUE. If FALSE only
runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where
the phenol is found. e.g. 0.1 = 10% of
the time.

Check the path in the next files:
/inputs/run_sugar.sh
vmd
hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

Beta color code in VMD.

Highest scored site
Middle scored site
Lowest scored site

Tutorial

Molecular dynamics

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

== You will get the following files: ==
inputs/
4mrhA_phe-opc_HMR-noWAT.prmtop
MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc
4mrhA_ref.pdb
parameters.in
run_sugar.sh
outputs/
cd44_10_14_FEN_DU/
molsites/
SS_Res_AT.pdb
overlaps/
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
restime/
SS_#_Res_AT.site
references/
5SC5-A.pdb
sugar_clusters_tcl/
main.tcl
overlap.tcl
parameters_example.in
parser.tcl
pru_main.tcl
qt_clustering.tcl
README.md
residence_time.tcl
solvent.tcl
sugar_driver.slurm.sh

You can open the parameter.in file and write the parameters of your choice.

FOLDNAME = cd44_10_14_FEN_DU # Folder Name
TRAJECTORY = MD-4mrhA_phe-opc_HMR-1us-FEN-noWAT.nc # FILE( *.nc or *.binpos)
TOPOLOGY = 4mrhA_phe-opc_HMR-noWAT.prmtop # FILE (*.parm7 or *.prmtop)
REFERENCE = 4mrhA_ref.pdb # FILE (*.pdb)
STEP = 10 # Indicates how often you want calculate
the cluster. Its expressed in frames per
nanosecond
CLUSTER_RADIUS= 1.4 # Indicates the radius from the dummy
atom center in which the phenols are
found, Armstrongs (float)
BINDING_SITE = resid 1 to 156 # Binding Site (atomselect VMD class)
SOLVENT = FALSE # Keep and run the algorithm for solvent
and cosolvent if TRUE. If FALSE only
runs cosolvent
SOLVENT_THRESHOLD= 0.1 # Lowest threshold to build pre-clusters.
COSOLVENT = FEN # atomselect VMD class
CS_ATOM_PROBE= DU,O1 # atomselect VMD class
COSOLVENT_THRESHOLD= 0.2 # Lowest threshold to build pre clusters.
N_CUT_RATIO = 0.1 # Percentage of the MD time where
the phenol is found. e.g. 0.1 = 10% of
the time.

Check the path in the next files:
/inputs/run_sugar.sh
vmd
hotspot directory path e.g yourpath/hotspots/

You can open the run_sugar.sh file and write the path of your choice. Usually, you should change the path where you have installed VMD and where you saved the sugar_clusters directory, they are highlighted in bold.

#!/bin/bash
rm sugar.out
time vmd -dispdev text -e yourpath/sugar_clusters_tcl/ main.tcl -args $@ > sugar.out 2>&1

sugar_clusters_tcl/main.tcl
set dir ”yourpath/hotspots/sugar_clusters_tcl”
You can open the main.tcl file and write your working directory path as highlighted in bold.

#set dir [lindex $argv 2]
set dir "yourpath/hotspots/sugar_clusters_tcl"

Run the script:
yourpath/hotspots/inputs/$ ./run_sugar.sh

Note: You can check the run status by opening the sugar.out file.

Open results and references in VMD.
Go to your outputs directory. There you will find the following files:
Outputs
References
5SC5-A.pdb
4mrhA_ref.pdb
cd44_10_14_FEN_DU
Molsites
SS_Res_AT.pdb
SS_Res_AT.csv
Overlaps
overlap_Res_AT.pdb
temp_Res_AT.pdb
rmsd_fit.csv
Restime
SS_#_Res_AT.site

Open VMD to analyze the results.

yourpath/hotspots/outputs/$ vmd -m receptor_ref.pdb 5SC5-A.pdb SS_Res_AT.pdb

Set the representations to analyze the results.

Representations > 4mrhA_ref.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > newcartoon
Representations > 5SC5-A.pdb > draw > liicorice
Representations > 5SC5-A.pdb > selection >resame ZJY HOH
Representations > SS_Res_AT.pdb > draw > VDW
Representations > SS_Res_AT.pdb > color > Beta

Beta color code in VMD.

Highest scored site
Middle scored site
Lowest scored site

Tutorial

Molecular dynamics

Save the parameters used during the MD simulations.

Parameter
Value
Note
Biomolecule
Protein
Type
proteinmask
e.g. 1-1446
It depends on the system
solventmask
WAT,FEN
Solvent Mask (WAT or WAT, ETA or WAT, FEN)
timemd
10,100, 1000…
MD (t) Nanoseconds in total
framexns
10,20, 50, 500…
Frames per nanosecond

Run the molecular dynamic simulations and save the following files:

File
Content
Note
receptor.prmtop
Parameter file
*.prmtop or *.parm7
receptor_ref.pdb
Reference file
*.pdb
receptor.nc
Trajectory file
*.nc or *.binpos

Solvent clusters.
Put the previous and the following files into the same directory:

Software/script
File
¿What is it?
Command
Note
VMD
VMD
Visual Molecular Dynamics
$ vmd
Change the path onto sugar_run.sh
Script
parameters.in
Script with parameters in tcl language to calculate clusters
$ vi parameters.in
It takes the *.prmtop, reference and trajectory files as input.
Has to be in the same directory as the MD results
Script
run_sugar.sh
Script to call VMD and to run the main.tcl script
$ ./run_sugar.sh
Has the instructions to find the clusters
Has to be in the same directory as the MD results

You have to have a directory with all necessary files to run the sugar cluster script.

Running phenol cluster algorithm:
Fill the file parameter.in as follow:

Command
Input
Note
FOLDNAME =
folder_name
Name of directory where results will be stored
TRAJECTORY =
receptor_cosolvent_results.nc
FILE( *.nc or *.binpos)
TOPOLOGY =
parameters_file.prmtop
FILE (*.parm7 or*.prmtop)
REFERENCE =
receptor_ref.pdb
FILE (*.pdb)
STEP =
10
step
We need to know how many frames we have. total frames/STEP.
CLUSTER_RADIUS =
0.6
FLOAT
BINDING_SITE =
resid 44 46 48 55 57 64 67
Binding Site (atomselect vmd class)
SOLVENT =
TRUE

SOLVENT_THRESHOLD =
0.1
Inferior edge for pre-clusters
COSOLVENT =
ETA
atomselect vmd class
CS_ATOM_PROBE =
O1, H1, C1
atomselect vmd class
COSOLVENT_THRESHOLD =
0.2

N_CUT_RATIO =
0.05
porcentaje de corte para armar los precluster

Run the job
$ ./run_ugar.sh

Visualization and analysis.
Once the run is finished a directory with name “folder_name” will be created at the work directory. Inside will be 3 new folders named Molsites, Overlaps, and Restime.

Directory
File
Content
Note
Work directory
sugar.out
Info about the run

Molsites
SS_Res_AT.pdb
File with Clusters info
Res= resid
AT = atom type
# = cluster number
Molsites
SS_Res_AT.csv
Site with cluster info
Overlaps
overlap_Res_AT.pdb
File with Overlap info
Overlaps
temp_Res_AT.pdb
File with Res time info
Overlaps
rmsd_fit.csv
File with rmsd dit info
Restime
SS_#_Res_AT.site
File with restime per cluster info

Sitios de Fenoles

2022-11-13T17:41:14Z

Rbetanzos: /* Introduction: */

Sitios de Fenoles

2022-11-13T17:40:10Z

Rbetanzos: Página creada con «=== Introduction: === The calculation of solvent site clusters allows to generate information related to the area, time, and type of interactions. That said, we present a brief tutorial for calculating solvent sites using the results of the molecular dynamics run with mixed solvents as input information. {| class="wikitable" style="margin:auto" |+ Pipeline Summary |- ! Header Step !! Description !! Input !! Output !! Note |- | Reference || PDB reference provides ||…»

Rafael Betanzos

2022-11-13T17:07:00Z

Rbetanzos: Página creada con «<H1>Rafael Betanzos San Juan</H1> Encargado del área de blah <H2>Educación</H2> <ol> <li>Ph.D. Química Biológica, Universidad de Buenos Aires. 2021 - Presente.</li> <li>M.C. Ciencias de la vida con orientación en Biomedicina y Bionanotecnología. Centro de Investigación Científica y de Educación Superior de Ensenada, 2017-2019.</li> <li>Bs.C. Agrobiotecnología. Universidad Tecnológica de la Selva, 2013-2017.</li> </ol> <H2>Experiencia lab…»

<H1>Rafael Betanzos San Juan</H1>

Encargado del área de blah

<H2>Educación</H2>
<ol>

<li>Ph.D. Química Biológica, Universidad de Buenos Aires. 2021 - Presente.</li>

<li>M.C. Ciencias de la vida con orientación en Biomedicina y Bionanotecnología. Centro de Investigación Científica y de Educación Superior de Ensenada, 2017-2019.</li>

<li>Bs.C. Agrobiotecnología. Universidad Tecnológica de la Selva, 2013-2017.</li>

</ol>

<H2>Experiencia laboral</H2>

<H2>Publicaciones</H2>

Servidores de interés

2022-11-13T17:05:22Z

Rbetanzos: /* En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. */

== En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. ==

{| class="wikitable" style="margin:auto"
|-
! Nombre !! Descripción !! Link
|-
| Molview || Dibujo de moléculas || https://molview.org/
|-
| Chemcad || Dibujo de moléculas|| https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#
|-
| Glycogit || Repositorio de versiones del glycogroup|| https://gitlab.com/glycodivision
|-
| Alpha fold 2 || Example || https://github.com/deepmind/alphafold#running-alphafold
|-
| PubChem|| Example || https://pubchem.ncbi.nlm.nih.gov/
|-
| PDB || Base de datos de Proteínas|| https://www.rcsb.org/
|-
| volkamerlab|| Example || https://projects.volkamerlab.org/teachopencadd/
|-
| NGL viewer|| Example || https://nglviewer.org/ngl/api/manual/molecular-representations.html
|-
| digitalocean|| Cómo configurar una autenticación en un servidor Linux a partir de una clave SSH || https://www.digitalocean.com/community/tutorials/how-to-configure-ssh-key-based-authentication-on-a-linux-server-es
|-
| Protein Plus || Cálculo de interacciones de ligandos|| https://proteins.plus/
|-
| Yeastgenome|| Example || https://www.yeastgenome.com
|-
| Biobicks|| Example || https://www.biobicks.org
|-
| Addgene|| Example || https://www.addgene.org
|-
| Bioparts|| Búsqueda de piezas biológicas|| https://www.bioparts.org
|-
| Bio Tools|| Información científica y técnica esencial sobre herramientas de software, bases de datos y servicios para la bioinformática y las ciencias de la vida.|| https://www.bio.tools
|-
| Biomaster || Example || https://www.biomaster-uestc.cn
|-
| Example || Example || https://2013.igem.org/Team:Paris_Bettencourt
|-
| Wormatlas || Example || https://www.wormatlas.org
|-
| Wormbase || Example || https://www.wormbase.org
|-
| Visual Stiduio|| Example || https://www.code.visualstudio.com/
|-
| Scopus || Example || https://www.scopus.com
|-
| Nematode|| Example || https://www.nematode.net
|-
| Stride Web|| Cálculo de porcentaje de estructuras secundarias || https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
|-
| Example || Corrección de imágenes para papers|| https://pacev2.apexcovantage.com/Upload
|-
| Seaborn || Plots en python|| https://seaborn.pydata.org/index.html
|-
| nglviewer|| Example || https://nglviewer.org/ngl/gallery/index.html
|-
| Amber|| Example || https://amber-md.github.io/pytraj/latest/index.html
|}

<h1>Información relacionada</h1>
<ol>
<li>[[Autor]]:[[Rafael Betanzos]]</li>
</ol>

Servidores de interés

2022-11-13T17:02:16Z

Rbetanzos: /* En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. */

Servidores de interés

2022-11-13T16:59:36Z

Rbetanzos: /* En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. */

== En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. ==

{| class="wikitable" style="margin:auto"
|-
! Nombre !! Descripción !! Link
|-
| Molview || Dibujo de moléculas || https://molview.org/
|-
| Chemcad || Dibujo de moléculas|| https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#
|-
| Glycogit || Repositorio de versiones del glycogroup|| https://gitlab.com/glycodivision
|-
| Alpha fold 2 || Example || https://github.com/deepmind/alphafold#running-alphafold
|-
| PubChem|| Example || https://pubchem.ncbi.nlm.nih.gov/
|-
| PDB || Base de datos de Proteínas|| https://www.rcsb.org/
|-
| Example || Example || https://projects.volkamerlab.org/teachopencadd/
|-
| NGLviewer|| Example || https://nglviewer.org/ngl/api/manual/molecular-representations.html
|-
| Example || Cómo configurar una autenticación en un servidor Linux a partir de una clave SSH || https://www.digitalocean.com/community/tutorials/how-to-configure-ssh-key-based-authentication-on-a-linux-server-es
|-
| Protein Plus || Cálculo de interacciones de ligandos|| https://proteins.plus/
|-
| Example || Example || https://www.yeastgenome.com
|-
| Example || Example || https://www.biobicks.org
|-
| Example || Example || https://www.addgene.org
|-
| Example || Example || https://www.bioparts.org
|-
| Example || Example || https://www.bio.tools
|-
| Example || Example || https://www.biomaster-uestc.cn
|-
| Example || Example || https://2013.igem.org/Team:Paris_Bettencourt
|-
| Wormatlas || Example || https://www.wormatlas.org
|-
| Wormbase || Example || https://www.wormbase.org
|-
| Visual Stiduio|| Example || https://www.code.visualstudio.com/
|-
| Scopus || Example || https://www.scopus.com
|-
| Nematode|| Example || https://www.nematode.net
|-
| Stride Web|| Cálculo de porcentaje de estructuras secundarias || https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
|-
| Example || Corrección de imágenes para papers|| https://pacev2.apexcovantage.com/Upload
|-
| Seaborn || Example || https://seaborn.pydata.org/index.html
|-
| Example || Example || https://nglviewer.org/ngl/gallery/index.html
|-
| Example || Example || https://amber-md.github.io/pytraj/latest/index.html
|}

Servidores de interés

2022-11-13T16:54:00Z

Rbetanzos: /* En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. */

= En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. =

{| class="wikitable" style="margin:auto"
|-
! Nombre !! Descripción !! Link
|-
| Molview || Dibujo de moléculas || https://molview.org/
|-
| Chemcad || Dibujo de moléculas|| https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#
|-
| Glycogit || Repositorio de versiones del glycogroup|| https://gitlab.com/glycodivision
|-
| Alpha fold 2 || Example || https://github.com/deepmind/alphafold#running-alphafold
|-
| PubChem|| Example || https://pubchem.ncbi.nlm.nih.gov/
|-
| PDB || Base de datos de Proteínas|| https://www.rcsb.org/
|-
| Example || Example || https://projects.volkamerlab.org/teachopencadd/
|-
| NGLviewer|| Example || https://nglviewer.org/ngl/api/manual/molecular-representations.html
|-
| Example || Cómo configurar una autenticación en un servidor Linux a partir de una clave SSH || https://www.digitalocean.com/community/tutorials/how-to-configure-ssh-key-based-authentication-on-a-linux-server-es
|-
| Protein Plus || Cálculo de interacciones de ligandos|| https://proteins.plus/
|-
| Example || Example || https://www.yeastgenome.com
|-
| Example || Example || https://www.biobicks.org
|-
| Example || Example || https://www.addgene.org
|-
| Example || Example || https://www.bioparts.org
|-
| Example || Example || https://www.bio.tools
|-
| Example || Example || https://www.biomaster-uestc.cn
|-
| Example || Example || https://2013.igem.org/Team:Paris_Bettencourt
|-
| Wormatlas || Example || https://www.wormatlas.org
|-
| Wormbase || Example || https://www.wormbase.org
|-
| Visual Stiduio|| Example || https://www.code.visualstudio.com/
|-
| Scopus || Example || https://www.scopus.com
|-
| Nematode|| Example || https://www.nematode.net
|-
| Stride Web|| Cálculo de porcentaje de estructuras secundarias || https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
|-
| Example || Corrección de imágenes para papers|| https://pacev2.apexcovantage.com/Upload
|-
| Seaborn || Example || https://seaborn.pydata.org/index.html
|-
| Example || Example || https://nglviewer.org/ngl/gallery/index.html
|-
| Example || Example || https://amber-md.github.io/pytraj/latest/index.html
|}

Servidores de interés

2022-11-13T16:48:44Z

Rbetanzos: /* En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. */

= En esta página encontrarás links a servidores de interés así como una breve descripción de los mismos. =

{| class="wikitable" style="margin:auto"
|-
! Nombre !! Descripción !! Link
|-
| Example || Dibujo de moléculas || https://molview.org/
|-
| Example || Dibujo de moléculas|| https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html#
|-
| Example || Example || https://gitlab.com/glycodivision
|-
| Example || Example || https://github.com/deepmind/alphafold#running-alphafold
|-
| Example || Example || https://pubchem.ncbi.nlm.nih.gov/
|-
| Example || Example || https://www.rcsb.org/
|-
| Example || Example || https://projects.volkamerlab.org/teachopencadd/
|-
| Example || Example || https://nglviewer.org/ngl/api/manual/molecular-representations.html
|-
| Example || Example || https://www.digitalocean.com/community/tutorials/how-to-configure-ssh-key-based-authentication-on-a-linux-server-es
|-
| Example || Example || https://proteins.plus/
|-
| Example || Example || https://www.yeastgenome.com
|-
| Example || Example || https://www.biobicks.org
|-
| Example || Example || https://www.addgene.org
|-
| Example || Example || https://www.bioparts.org
|-
| Example || Example || https://www.bio.tools
|-
| Example || Example || https://www.biomaster-uestc.cn
|-
| Example || Example || https://2013.igem.org/Team:Paris_Bettencourt
|-
| Example || Example || https://www.wormatlas.org
|-
| Example || Example || https://www.wormbase.org
|-
| Example || Example || https://www.code.visualstudio.com/
|-
| Example || Example || https://www.scopus.com
|-
| Example || Example || https://www.nematode.net
|-
| Example || Example || https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
|-
| Example || Example || https://pacev2.apexcovantage.com/Upload
|-
| Example || Example || https://seaborn.pydata.org/index.html
|-
| Example || Example || https://nglviewer.org/ngl/gallery/index.html
|-
| Example || Example || https://amber-md.github.io/pytraj/latest/index.html
|}

Servidores de interés

2022-11-13T16:41:09Z

Rbetanzos: links a servidores de interés

Docking sesgado

2022-05-18T13:42:14Z

Rbetanzos: Página creada con «Hola mundo Para correr las dinámicas utilizamos la siguiente secuencia de paso con su correspondiente script. Minimización • min.mdin Termalización 1 • terma1.mdin Termalización 2 • terma2.mdin Equilibración 1 • equil1_pcte_5ns.mdin Equilibración 2 • equil1_pcte_10ns.mdin Dinámica Molecular Plana • MD-ntp_10-ns.mdin Comentarios: En los scripts se encuentra un parámetro nombrado restraintmask: Nosotros utilizamos ese parámetro para re…»

Hola mundo

Para correr las dinámicas utilizamos la siguiente secuencia de paso con su correspondiente script.

Minimización
• min.mdin

Termalización 1
• terma1.mdin

Termalización 2
• terma2.mdin

Equilibración 1
• equil1_pcte_5ns.mdin

Equilibración 2
• equil1_pcte_10ns.mdin

Dinámica Molecular Plana
• MD-ntp_10-ns.mdin

Comentarios:
En los scripts se encuentra un parámetro nombrado restraintmask: Nosotros utilizamos ese parámetro para restringir sólo los átomos del backbone. Por tanto, le indicamos al programa que tome el número de @CA de acuerdo al número de residuos. e.g. ':1-173@CA'. para una proteína compuesta por 173 residuos.

Usuario:Rbetanzos

2022-04-29T20:42:03Z

Rbetanzos:

¿Cómo crear una página en esta wiki?

2022-04-29T20:37:44Z

Rbetanzos: Página creada con «Esta página esta diseñada para ayudar en la creación de páginas en esta wiki.»

Esta página esta diseñada para ayudar en la creación de páginas en esta wiki.

Usuario:Rbetanzos

2022-04-29T20:36:05Z

Rbetanzos:

<H1>Rafael Betanzos San Juan<H1>

Encargado del área de blah

<H2>Educación<H2>

<H2>Experiencia laboral<H2>

<H2>Publicaciones<H2>

Usuario:Rbetanzos

2022-04-29T20:35:13Z

Rbetanzos:

<H1>Rafael Betanzos San Juan
Encargado de

<H2>Educación<H2>

<H2>Experiencia laboral<H2>

<H2>Publicaciones<H2>

Usuario:Rbetanzos

2022-04-29T20:34:55Z

Rbetanzos:

<H1>Rafael Betanzos San Juan <H1>
Encargado de

<H2>Educación<H2>

<H2>Experiencia laboral<H2>

<H2>Publicaciones<H2>

Usuario:Rbetanzos

2022-04-29T20:34:33Z

Rbetanzos: Página creada con «<H1>Rafael Betanzos San Juan <H1> <H2>Educación<H2> <H2>Experiencia laboral<H2> <H2>Publicaciones<H2>»

<H1>Rafael Betanzos San Juan <H1>

<H2>Educación<H2>

<H2>Experiencia laboral<H2>

<H2>Publicaciones<H2>