Re: Atom selection in Tcl Force script with Amber partop file

From: Daniel Torrente (danieltorrenteq_at_gmail.com)
Date: Fri Aug 15 2014 - 18:21:23 CDT

Dear Maxim,

Thanks for your help, it works perfectly. I will put all the steps for
future reference (the least that I can do).

On VMD (PDB loaded with the beta 1 and 2 atoms)

set sel1 [atomselect top "beta == 1"]
set sel2 [atomselect top "beta == 2"]

#### For the beta 1 set of atoms #####
set ch1 [open beta1.txt w]
puts $ch1 "[$sel1 get Index]"; # single line with serial numbers (1-based
indicies)
close $ch1
#################################

#### For the beta 2 set of atoms #####
set ch2 [open beta2.txt w]
puts $ch2 "[$sel1 get Index]"; # single line with serial numbers (1-based
indicies)
close $ch2
#################################

Tcl force
###############Replace the atom selection part of the Tcl force script for
this ########
# Atoms selected for force application

set ch1 [open beta1.txt r]
set atomindex1 [read $ch1]
close $ch1

set ch2 [open beta2.txt r]
set atomindex2 [read $ch2]
close $ch2

set a1 [addgroup $atomindex1]
set a2 [addgroup $atomindex2]

#########################

Thanks again, my weekend was saved

Daniel

2014-08-15 16:48 GMT-05:00 Maxim Belkin <mbelkin_at_ks.uiuc.edu>:

> Daniel,
>
> VMD can help. You can load your pdb file into VMD and make two selections:
>
> set sel1 [atomselect top "beta == 1"]
> set sel2 [atomselect top "beta == 2"]
>
> then write their serial numbers into text files like that:
>
> set ch [open beta1.txt w]
> puts $ch "[$sel1 get serial]"; # single line with serial numbers (1-based
> indicies)
> close $ch
>
> # and similar three lines for $sel2
>
> Then, in your tcl script simply read these files
>
> set ch [open beta1.txt r]
> set atomindex1 [read $ch]
> close $ch
>
> # and, again, similar one for beta2.txt
>
> At this point you have atomindex1 (and atomindex2) and can use addgroup,
> or anything you want.
>
>
>
> Maxim
>
>
> On Aug 15, 2014, at 12:25 PM, Daniel Torrente <xlb608_at_my.utsa.edu> wrote:
>
> Dear NAMD user,
>
> I am trying to calculate the PMF between two proteins by means of SMD
> simulations using amber ff. My problem is related with the selection of the
> pulling atoms in the Tcl script using the amber par-top file. Since the
> amber par-top file do not has segname information is there other way to
> define the pulled atoms in the Tcl script that is compatible with the amber
> par-top file?
>
> This question was asked a long time ago but is still without an answer.
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2005-2006/0196.html
>
> Thanks in advance,
>
> Daniel
>
> Here is the usual way to define the pulling atoms in SMD/Tclforce.
> ###################
> set targets1 {}
> set targets2 {}
> set inStream [open ionized_SMD2.pdb r]
> foreach line [split [read $inStream] "\n"] {
>
> set type [string trim [string range $line 0 5]]
> set name [string trim [string range $line 12 15]]
> set resid [string trim [string range $line 22 25]]
> set beta [string trim [string range $line 60 65]]
> set segname [string trim [string range $line 72 75]]
>
>
> if { $beta == 1.00 } {
> lappend targets1 "$segname $resid $name"
> }
> if { $beta == 2.00 } {
> lappend targets2 "$segname $resid $name"
>
> }
> }
> close $inStream
>
> set atoms1 {}
> foreach target1 $targets1 {
> foreach {segname resid atom} $target1 { break
> }
>
> set atomindex1 [atomid $segname $resid $atom]
> lappend atoms1 $atomindex1
> }
>
> set atoms2 {}
> foreach target2 $targets2 {
> foreach {segname resid atom} $target2 { break
> }
>
> set atomindex2 [atomid $segname $resid
> $atom]
> lappend atoms2
> $atomindex2
>
> }
>
> set a1 [addgroup $atoms1]
> set a2 [addgroup $atoms2]
> ########################
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:43 CST