From: Sabuj P. <sab...@va...> - 2005-03-19 21:48:26
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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...@bi...) > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |