RE: pKa calculation with thermodynamic integration (TI)

From: Radak, Brian K (
Date: Wed May 17 2017 - 09:54:39 CDT

You can do all of this from inside psfgen now:

patch GLUHD <segid:resid>
regenerate angles dihedrals

set atom0List {CG HG1 HG2 CD OE1 HE1 OE2 HE2}
foreach atom0 $atom0List {
  set atom1 [format "%d1" $atom0] ; # this only works bc of the arbitrary naming convention in the patch
  psfset beta $atom0 -1.0
  psfset beta $atom1 1.0

writepsf <psfname>
writepdb <pdbname> ;# this assigns atom indices to all of the atoms

set ebondsfile [open "foo.extrabonds" "w"]
foreach atom0 $atom0List {
  set atom1 [format "%d1" $atom0] ;
  set i [expr {segment atomid <segid> <resid> $atom0] - 1}] ;# note the index shift
  set j [expr {segment atomid <segid> <resid> $atom1] - 1}]
  puts $ebondsfile [format "bond %d %d %f %f" $i $j 100.0 0.0]
close $ebondsfile

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

From: [] on behalf of Hannes Loeffler []
Sent: Wednesday, May 17, 2017 3:37 AM
To:; Sadegh Faramarzi Ganjabad
Subject: Re: namd-l: pKa calculation with thermodynamic integration (TI)

> Is that what I am supposed to do? if so, how can I tight (for
> example) CD and CD1 atoms together by a harmonic restraint? at the
> beginning, there is no distance between them.

You need to mark the outgoing group with -1 in the column that you have
chosen (alchCol). Look into the extraBonds feature to set additional


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