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 "I suspect...
View ArticleHow do I auto generate multiple VMD representations from a list of ids in tcl...
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...
View ArticleTcl 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.xtcset final [atomselect top "not (water or ions or resid 1216)" frame last]$final writepdb...
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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 named...
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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...
View ArticleWriting Python or TCL VMD scripts [closed]
Does anyone know a complete tutorial to learn about writing Python or TCL scripts?I want to write a script to load a molecule , make 3 representations of it,and change attributes(like coloring method,...
View ArticleTCL (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...
View Articlevmd-1.9.4a57 compile error: typedef redefinition with different types ('void'...
I'm compiling vmd-1.9.4a57 on macos 12 (ventura) but can't get rid of this problem:Compiling colvarproxy_vmd.C --> colvarproxy_vmd.o ...clang: warning: argument unused during compilation:...
View ArticleImportError 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...
View ArticleAbout 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...
View ArticleDefault Representation/Drawing method in VMD
In VMD I want to load every new file with the drawing method CPK. This doesn't seem not to be an option in the .vmdrc file for some technical reasons. How can I do this from the VMD command line (so...
View ArticleIs 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...
View ArticleFor loop of bash script not working, reading lthe next lines within the...
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 be...
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