Please see:
http://chips.csb.ki.se/pymol/msg02737.html
..even after using the server at http://nbcr.sdsc.edu/pdb2pqr/index.html
and generating a pqr file, apbs still may not work. e.g. I have this
problem with PDBID: 1TF7.
Too bad there is no grasp for linux (its really fast for a general
electrostatics overview), and well i can't get the delphi source to
recompile for larger sets of atoms on linux using g77.
I hope this helps and that the apbs server works for you.
..Sabuj Pattanayek
fredb wrote:
Hi Everyone,
When I try to use PyMol and APBS (according to the instructions on
Michael Lerner's web page,
http://www-personal.umich.edu/~mlerner/PyMOL/) to display an
electrostatic potential surface, I get a few errors (see output that
follows). Does anyone know why this is happening and how to fix it?
I'm using RedHat 9.0, PyMol v. 0.97
Thanks,
Fred
coarsedim is [131.55450687408447, 133.26979846954345, 121.22360420227051]
finedim is [97.385004043579102, 98.393999099731445, 91.308002471923828]
center is [57.759501457214355, 49.317999839782715, 78.048002243041992]
finegridpoints is [225, 225, 193]
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
WARNING: 124 atoms did not have formal charges assigned
WARNING: 305 atoms did not have properties assigned
--
APBS -- Adaptive Poisson-Boltzmann Solver
Version 0.3.2
Nathan A. Baker (ba...@biochem.wustl.edu)
Dept. Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Additional contributing authors listed in the code documentation.
Copyright (c) 2002-2004. Washington University in St. Louis.
All Rights Reserved.
Portions Copyright (c) 1999-2002. The Regents of the University of
California.
Portions Copyright (c) 1995. Michael Holst.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
--
APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation
numerically. FEtk and PMG are developed and maintained by the Holst
Research Group at UC San Diego. PMG is designed to solve the nonlinear
Poisson-Boltzmann equation and similar problems with linear space and
time complexity through the use of box methods, inexact Newton methods,
and algebraic multilevel methods. FEtk is designed to solve general
coupled systems of nonlinear partial differential equations accurately
and efficiently using adaptive multilevel finite element methods,
inexact Newton methods, and algebraic multilevel methods. More
information about PMG and FEtk may be found at http://www.FEtk.ORG.
--
This executable compiled on Nov 10 2004 at 10:51:17
Vio_ctor2: Gethostbyname fail INET sock dueto VIO_UNKNOWN_ERROR(0)
Parsing input file pymol-generated.in...
parsePBE: Warning -- parsed deprecated bcfl 1 statement
parsePBE: Please use bcfl sdh instead.
NOsh: Warning -- parsed deprecated statment chgm 1.
NOsh: Please use chgm spl2 instead!
parsePBE: Warning -- parsed deprecated srfm 1 statement.
parsePBE: Please use srfm smol instead.
parsePBE: Warning -- parsed deprecated calcenergy 0 statement.
parsePBE: Please use calcenergy no instead.
parsePBE: Warning -- parsed deprecated calcforce 0 statement.
parsePBE: Please use calcforce no instead.
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
Vio_ctor2: Gethostbyname fail INET sock dueto VIO_UNKNOWN_ERROR(0)
Valist_readPDB: Unable to parse resSeq token (A) as int!
Valist_readPDB: Error while parsing residue name!
Valist_readPQR: Error parsing ATOM field!
Error while reading molecule from pymol-generated.pqr
Error reading molecules!
ObjectMapLoadDXFile-Error: Unable to open file!
---
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