[gmx-users] apbs : pqr file generation problem

[Kai Zhuang]

i tried -grasp and -mead options,
and this time i tried by using pdb2pqr server, then use the
command-line program instead of using the plugin.
My command is:
/sw/bin/powerpc-apple-darwin8.2.0/apbs 11230963927.in > ZKH_apbs.out

Resulting in:
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
apbs(1763) malloc: *** vm_allocate(size=2084835328) failed (error code=3)
apbs(1763) malloc: *** error: can't allocate region
apbs(1763) malloc: *** set a breakpoint in szone_error to debug
VASSERT: ASSERTION FAILURE!  filename vmem.c, line 245, (ram != ((void *)0))
Abort

If i try it in PyMol Plugin, i get the same error as before. saying
that there's a lot of atoms without formal charges assigned to it.

On 8/3/05, David <spoel at xray.bmc.uu.se> wrote:
> 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.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 


-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
6478314789