From: Peter Freddolino (
Date: Mon Mar 07 2011 - 09:19:20 CST

Hi Francesco,

On 03/07/2011 01:12 AM, Francesco Pietra wrote:
> this led to the added proton being in the unfavorable position that I
> described, although the psf/pdb could be minimized and heated.

Could you elaborate on how unfavorable this position seems? What's wrong
with it? Unless you have something truly pathological, a minimization
should give you an appropriate orientation. psfgen has no knowledge of
the force field, so it won't even try to place the hydrogen in a way
that forms hydrogen bonds.
> Previously, I also filled in "Autopsf - Add Patch", in addition to the above,
> Segment 2 (opt) ... Residue 2:....
> for the intended acceptor of Segment 1, Residue 1
> at no avail as far as the H-bond is concerned. This latter action in
> an imitation of the DISU patch, where both S atoms of the S-S bond are
> set in.

Specifying a second residue does no good whatsoever... the topology
entry that you're using only acts on one residue.

> ************
> What I hope is that there is a mistake in my procedure, and be
> corrected about. Otherwise suggestions how to set correctly H-bonds in
> VMD/NAMD along a different route. As I said, I came to NAMD with
> correct PDB files - from REDUCE or other - as far as H-bonds are
> concerned. However, files strictly respecting PDB rules and, in
> addition, also with some non CHARMM naming, which I tried to correct.
> I was unable to arrive at workable psf/pdb along this route. Finally,
> I could also correct the autopsf.pdb by repositioning the proton in
> between GLU and the acceptor, be that the conjugate base or Cl-, with
> a graphic package. However, this also failed - in my hands - to arrive
> at workable psf/pdb.

You would again need to give more details on what you tried to do and
what errors occurred in order to get help.