[gmx-users] apbs : pqr file generation problem

Kai Zhuang kai.zhuang at gmail.com
Wed Aug 3 19:06:31 CEST 2005


I ran a MD simulation, and i wanted to study the resulting structure's
electrostatic potential map.  so to do this, parsed out the last frame
as pdb with trjconv and then used PyMol's APBS plug-in with option to
let PyMol generate Hydrogen and Terminies.  There's a PQR file
generated but APBS complained that there's 89 atoms missing charges
and calculation wasn't able to ran.  I went to PDB2PQR server and
converted the pdb file to pqr file there.
When i loaded it in APBS, nothing happened and eventually it told me
to load another PQR file.

am i missing something here?  i'm guessing PDB2PQR doesn't generate a
good pqr file in this case.  Maybe it's because it's designed for
processing AMBER file not gromacs?

any ideas?

thanks in advance
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com

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