Re: hBond colvars and patching

From: Giacomo Fiorin (
Date: Sun Mar 06 2011 - 22:57:04 CST

Hi Francesco, use the hBond colvar component only if you need to apply a
restraint or compute the potential of mean force for breaking / forming that
hydrogen bond.

But the starting point should always be a reasonable protonation state, if
that's not the most stable for any reason, there isn't a restraint that can
fix that.

Do you think it's the former or the latter? If you run without any
additional restraints (colvars or not) and the structure is not stable, then
the protonation state is not good, and that should be corrected regardless.


---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
---- ----

On Sun, Mar 6, 2011 at 3:05 PM, Francesco Pietra <>wrote:

> Hello:
> lost my mail, taken the essential from the VMD archive.
> <<in setting "hBond" in colvars for GLUP-GLU and
> GLUP-chloride_anion hydrogen bonds, should the acidic proton of
> neutral GLU be present in the PDB file, as obtained from GLUPP
> patching?>>
> This question arose from my problems in getting the correct
> orientation of the added proton. I have now recreated the psf/pdb from
> scratch and - in all cases - the added proton goes into the least
> favorable position with respect to the intended acceptor. As the
> H-bond is indirectly evident from my 2A X-ray diffraction data, and
> the importance of the H-bond is clearly shown by my physiological
> experimentation at different pH values (and the good ones suggest 50%
> protonation of GLU), I am quite concerned. If it is an error in my
> procedure, I would be happy, however patching does not leave much room
> for intervention. This is why I tried to come to NAMD with already
> protonated titrable residues, got from REDUCE or other software, or by
> adjusting the conformations manually on psf/pdb, which created
> problems to NAMD.
> What happens (both toward ASP or other acceptor) is that the acidic
> proton is anti to the desired acceptor. In one case it is on the
> "wrong" oxygen, thus even farther away. Interatomic distances and
> orientations from X-ray diffraction data are standard for stron
> H-bonds.
> Before redoing psf/pdb, I had minimized and heated the ensemble in
> lipid bilayer surrounded by TIP3. Should the correct orientation in
> H-bond result from extensive MD?
> thanks
> francesco pietra
> Assuming correct procedure, how now with hBond colvar? Should that put
> the matter in order, or hBond colvar is to be used in place of GLU
> patching?

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