Questions tagged [vmd]
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
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For loop of bash script not working, reading lthe next lines within the previous loop [duplicate]
I cannot solve the for loop error in bash script.
The bash script is for extracting data from remote server, copying mapped files locally, and then executing a tcl script.
The above process should ...
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Is there a way to use tcl to customize and isolate selected atoms in VMD?
I am attempting to write a script that isolates beads of a certain name and adjusts their draw style before running the trajectory animation and taking a snapshot of the final configuration. the ...
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About making animation by VMD(Visual Molecular Dynamics)
~Details~
I have a file.pdb that contains 10 frames but each frame don’t have same data size(ex. frame1 has 10 atoms, frame2 has 20 atoms….).
I need a way to make animation of this file, but VMD ...
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ImportError When Attempting to Use VMD After Installation
I recently attempted to use the Variational Mode Decomposition (VMD) package in Python. After successfully installing the package with the command pip install vmd, I tried to import it into my project ...
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TCL (VMD scripts) functions in python
I have access to a bunch of TCL scripts but some of them are not working fast and I want to convert some of them to python. Does anybody have any experience? ex. one of the functions that I faced ...
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Tcl foreach loop not finding second variable
I am sure this has been asked here before but I can't seem to find any link that can help me with my particular problem.
I am using tcl scripting within vmd to do a quick analysis.
package require ...
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Tcl print cwd and use it as string
I was making a small script in tcl for VMD:
mol load psf run_1/structure.psf xtc run_1/postDocking_wrapped.xtc
set final [atomselect top "not (water or ions or resid 1216)" frame last]
$...
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How do I auto generate multiple VMD representations from a list of ids in tcl script
I am new to tcl. I have the basics down but I hope to get better. I have a list of lists of ids that I want to select from a molecule for visualization. I want to apply different coloring to each rep ...
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Confused with psfgen module of VMD
I am fairly new to VMD and programming in general.
I need to combine two pdb files of subunits into a combined pdb and psf file with both subunits.
I used the Namd tutorial and used two pdb files ...
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Tcl Unmatched open quote in list. VMD MMPBSA error
I've been trying to run MMPBSA calculations using CAFE, however, when I use -pb_rad charmm. VMD prints the following error when it begins to run PB calculations:
"Unmatched open quote in list &...
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TK/TCL console does not run full script, but works with manual input
New programmer here. I have been trying to run my script through Tk console through a VMD program which works when I copy it into tkconsole, however when I source/load my script into tkconsole, it ...
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How to calculate the average of each column with Tcl script
I need to calculate the average of each column with a tcl script from a text file please help me
Frame Time Elec VdW Nonbond Total
0 0 -216.63 -16.0174 -232.647 -...
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finding difference between list elements in Tcl
I am a beginner in using Tcl. I am using it as VMD (molecular visualization) software uses it as a scripting language.
I have a list of co-ordinates of atom positions for a protein like: {{1 2 3} {7 9 ...
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Controlling external program with python
for my studies I need to process a lot of data. The data needs to be analyzed by a program called VMD and should finally be stored in an excel sheet. My aim is to automate the whole process instead of ...
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Use proc from inside another proc on TCL
I'm trying to write a script in tcl to execute some analysis on VMD. First I'm creating an atom selection inside a procedure, then I'm trying to use it on another procedure.
The atom selection from ...
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