From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 13 2014 - 02:56:03 CDT
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.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von zeynab mohamad hoseyni
Gesendet: Freitag, 13. Juni 2014 07:53
An: namd-l_at_ks.uiuc.edu
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
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