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Hey all for a program I am working on it uses pdb (protein data bank) files and computes the distance between all atoms from one another. I have a code that does this, however my personal and work computers don't have enough computing power to fully execute the program without crashing the program I run it in (VMD- Visual Molecular Dynamics). I do however have access to a supercomputer, but it only runs perl scripts. The code is written for the VMD extension TK console. Is there a way that I can use perl to execute my tk console code? below is the code:

set seg1 [atomselect top "segname LA0 and name CA"]
set seg2 [atomselect top "segname RA0 and name CA"]

set file [open "Contact_map27.dat" w]

set list1 [$seg1 get index]
set list2 [$seg2 get index]

foreach atom1 $list1 {
       foreach atom2 $list2 {
            set index1 [atomselect top "index $atom1"]
            set index2 [atomselect top "index $atom2"]
            set resid1 [[atomselect top "index $atom1"] get resid]
            set resid2 [[atomselect top "index $atom2"] get resid]
            set resnm1 [[atomselect top "index $atom1"] get resname]
            set resnm2 [[atomselect top "index $atom2"] get resname]
 puts $file "$resnm1 $resid1 $resnm2 $resid2 [veclength [vecsub [measure center $index1] [measure center $index2]]]"
            $index1 delete
            $index2 delete
    }
}

close $file

This does the computation on the pdb file that is loaded into VMD. Any help or suggestions would be much appreciated.

Heather Lynn
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1 Answers1

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So, you are trying to do analysis of each trajectory (DCD) file? Maybe it is not the best idea, but to separately each frame as PDB and make analysis of every PDB file? It won't require too powerful PC. So, if supercomputer can run VMD (it has to run it for DCD file analysis), so it will be possible to run TCL scripts.

MD provides embedded scripting languages (Python and Tcl) for the purpose of user extensibility.

Source

XuMuK
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