From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Mon Jun 16 2014 - 11:20:46 CDT
Hi Norman,
In addition to the way to suggested here, which works very well, the tcl force tutorial has provided another way
(Example 3: Forcing a Subset of Atoms ,TclForces )
TclForces
TclForces
View on www.ks.uiuc.edu Preview by Yahoo
through which you may introduce a target pdb, marking all the side-chains you are interested in and then opening
the pdb, reading the lines and extracting the atoms in each side-chains in order to refer to them in the next steps.
I was wondering which way is more efficient, specially in the case that you need to apply force on the side-chains of all residues containing in the protein (397 residues in my case)?
I went through the way you suggested here and it works very slowly. I'm looking for a way to improve the efficiency
significantly and I wonder if you can guide me.
Thanks in advance,
Zeynab
On Friday, June 13, 2014 9:26 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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