hBond colvars and patching

From: Francesco Pietra (
Date: Sun Mar 06 2011 - 14:05:47 CST

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

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

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?

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

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