Atom selection in Tcl Force script with Amber partop file

From: Daniel Torrente (xlb608_at_my.utsa.edu)
Date: Fri Aug 15 2014 - 12:25:49 CDT

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]
########################

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