Re: AW: How to refer to side-chain via tcl-force scripting?

From: zeynab mohamad hoseyni (
Date: Fri Jun 13 2014 - 03:21:08 CDT

Hi Norman, Looks great! thanks! just one more question: sourcing the tcl through the tcl-force script is different from to write it down directly in the tcl-force script? Because when I write it down directly I receive the error from which I defer that the script can not realize the commands regarding the side chain.. All the Best, Zeynab On Friday, June 13, 2014 8:56 AM, Norman Geist <> wrote: Guess no! A good way to do it, is do write a TCL script for VMD to prepare some kind of config file containing the information you need and source this configuration within your TCLForces script. Like (expects to have a molecule loaded already):   prepare.tcl:   puts “Input) Molid?” gets stdin molid puts “Input) Resids?” gets stdin resids   array unset sidechains; #save restart array set sidechains {} foreach resid $resids {                 set sel [atomselect $molid “resid $resid and sidechain”]                 set sidechains($resid) [$sel get index]                 $sel delete }   set fp [open “prepared.conf.tcl” w] puts $fp [list array set sidechains [array get sidechains]] close $fp puts “Info) Done, you’re are now prepared!”   So within your TclForces script:   source prepared.conf.tcl #loop over sidechains foreach resid [array names sidechains] {                 puts “Now doing something with sidechain of resid $resid having this atoms: $sidechains($resid)” }   Norman Geist. [] Im Auftrag von zeynab mohamad hoseyni Gesendet: Freitag, 13. Juni 2014 07:53 An: Betreff: namd-l: How to refer to side-chain via tcl-force scripting?   Dear all,   I need to impose force on the side-chain of some residues, using tcl-force scripting. Do you know if the tcl-force interface provides any command so that you can refer to side-chain of the desired residue?   Thanks in advance for your help, Zeynab ________________________________ Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.

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