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

From: Peter Freddolino (
Date: Tue Mar 08 2011 - 13:48:53 CST

Hi Francesco,

On 03/08/2011 01:34 AM, Francesco Pietra wrote:

> No matter what I do, be that pure MD simulation, biased MD simulation,
> or docking simulation, I do not move further if the system is not
> equilibrated - or amenable to equilibration - assuming that the
> equilibrated ensemble is the closest to nature. My suspicion - at the
> moment - is that the what I am using does not treat H-bonding
> properly. I'll report to you the result of equilibration of my
> ensemble, starting from what autopsf allows to do, i.e., with
> remaining "syn" situations.

I am, emphatically, **not** saying that you should ignore either the
experimental results or chemical expectations on your system regarding
protonation states. All that I am saying is that the method that you
have been using (simply applying a protonation patch with psfgen) is not
the correct way to get the hydrogen bonds that you expect, because it
doesn't pay any attention to anything but its internal coordinate
tables. All I'm suggesting is that you're spending a lot of time
worrying about something (proton orientations) that should be rapidly
fixed by pretty much any system preparation protocol during minimization
or early equilibration. Ifn as you sayn you don't move on until your
system is equilibrated. I'm also suggesting that you may want to do
something more quantitative than manually determining which residues
should be protonated (using something like propka designed for that
purpose would not be a bad idea).

> Thanks for the suggestion. I never used molefacture in VMD, it is the
> right time now to learn it. However, from what I did in between my
> last mail and your present answer, I am unsure whether any adjustment
> of stereochemistry will solve the issue. I suspect (though I hope to
> be wrong) that top_all27_prot_lipid.rtf (edited for the problem of H-H
> into TIP3) I used in autopsf has an idiosyncrasy for H-bonds, at least
> when interatomic distances are short (though perfect for H-bonds). In
> fact, when the stereochemistry is adjusted to "syn" by the protocol I
> have shown, autopsf brings back to "anti" most situations, except
> those for the longer H-bonds.

Why are you regenerating the psf again? It is not necessary to do so if
you only changed the coordinates. With that said, as long as you didn't
change the name of one of your atoms, psfgen shouldn't move them... did
it, and if so, can you send me input and output files?


>> Best,
>> Peter
>>> 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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