Re: vmd-l: Re: hBond colvars and patching

From: Peter Freddolino (
Date: Mon Mar 07 2011 - 17:08:23 CST

On 03/07/2011 11:04 AM, Francesco Pietra wrote:
> Hello Peter:
> Thanks for answering. Please, see below.
> On Mon, Mar 7, 2011 at 4:19 PM, Peter Freddolino <> wrote:
>> 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.
> Attached please see a picture of a GLU-ASP couple. At OE2 (highlighted
> in cyan) of GLU I have attached a second proton (syn to ASP), at 180
> deg from the original one (anti to ASP). That should illustrate that
> the original placement of the proton is unfavorable for H-bonding with
> ASP. Minimization should not (I guess) place the proton syn to ASP
> because the original anti position has no unfavorable interactions.

psfgen is doing its job here: place all atoms according to the
definitions in the topology file. Moving atoms around further due to
energetic considerations is a job for minimization or dynamics. If
you're planning on doing what people typically do with these structures
(running MD) this should not present a problem. If you're going to do
something like docking and want a relaxed conformation, you'll need to
run a short equilibration anyway. Do note that you don't *know* that the
hydrogen rotation gives you the lowest energy structure anyway; there
may also be some rotation of one or both of the involved residues as well.

> I am now trying again to set up in the pdb file from autopsf what I
> believe is the correct stereochemistry, to run autopsf again. Maybe I
> did a mistake in a previous similar attempt. However, I would be not
> too much surprised that the matter can be tackled differently. These
> are problems that people should have encountered each other day.

A much better solution, if you really must have a starting structure
with those hydrogens oriented the way you think they should be, is just
to modify the coordinates in the pdb, and leave your psf the way it is.
You should be able to do this either using molefacture, or with a little
tcl scripting by using the standalone code discussed at


> Thanks a lot
> francesco
>>> ************
>>> 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.
>> Best,
>> Peter

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