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! ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
