[gmx-users] apbs : pqr file generation problem

David spoel at xray.bmc.uu.se
Wed Aug 3 19:18:51 CEST 2005

On Wed, 2005-08-03 at 13:06 -0400, Kai Zhuang wrote:
> Hi,
> 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?

You can try editconf with two options -mead or -grasp (maybe you need
CVS code)
> any ideas?
> thanks in advance
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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