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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 13 2014 - 03:26:33 CDT

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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