From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Sat Jun 14 2014 - 09:03:09 CDT
Hi Tristan,
No worries..! every comment is always useful ! If you look at the script provided by Norman,
there you can find out how your comment has been employed too..! :-)
Thanks again for your participation..
All the Best,
Zeynab
On Saturday, June 14, 2014 1:51 PM, Tristan Croll <tristan.croll_at_qut.edu.au> wrote:
Hi Zeynab,
It seems this was a more complex problem than I realised, and didn’t deserve my flippant and dismissive response. Please accept my apologies.
Best regards,
Tristan
From:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of zeynab mohamad hoseyni
Sent: Saturday, 14 June 2014 2:02 PM
To: Norman Geist
Cc: Namd Mailing List
Subject: Re: AW: AW: namd-l: How to refer to side-chain via tcl-force scripting?
Hi Norman,
Thanks a lot..! The script is working very well..
All the Best,
Zeynab
On Friday, June 13, 2014 9:36 AM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
You need to source the prepare script to VMD. Afterwards source the resulting conf file within TCL forces and work with the “sidechains” array.
Norman Geist.
Von:zeynab mohamad hoseyni [mailto:zmhoseyni_at_yahoo.com]
Gesendet: Freitag, 13. Juni 2014 10:21
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: AW: namd-l: How to refer to side-chain via tcl-force scripting?
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 <norman.geist_at_uni-greifswald.de> 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.
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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