From: Raul Araya (
Date: Fri Jun 01 2007 - 23:55:33 CDT

Dear VMD users:

This is a long question:

I am working with electrostatic potential and MMPBSA calculations with a
protein at pH 7 and 6.0 so in order to obtain the pH efect on the
protonation state of the residues of the protein I'm using PRO-PKA and
PDB2PQR in standalone mode, but later I want to create psf files with
PSF_GEN/VMD to use the resulting files on NAMD. The problem goes as follow:

--The PQR file I get is made with the CHARMM force field and CHARMM names
for atoms and residues, so the CYS atoms that are involved in SS bonds are
named as 1CB and 1SG and in the residue ID column the DISU name appears
--For some protonated ASP the HD2 hydrogen is added and the ASPP name
appears for some atoms in the RES-ID column (the same for the GLU protonated
with the name GLUP).
--The problem is that when I want to generate the PSF files with psfgen from
VMD if I apply patches there are some atoms for which psfgen cannot assign
coordinates, also in some cases is unable to recognize the ASPP or DISU
--So my question is should I?
            1) rename those residues to read CYS instead of DISU and CB
instread of 1CB and the assing patches for them (the same for the ASSP -->
ASP and GLUP --> GLU) and run psfgen without guesscoord command ??
            2) create pdbs without Hydrogens and then rename the residues
and then remane the atoms and residues, apply psfgen with patches and
guesscoord ??

--Or any other suggestion ???

Please Help, if the idea or question is not well understood or explained,
please let me know because this is very important for me and I want to ask
for help in the most clear way...

Raul Araya
Universidad de Chile.