Hi, I just want to use pymol+apbs and do some calculation on protein
(PDB 1cse ).
Unfortunately, I got the error msg in the following.
This PyMOL(TM) Incentive Product is Copyright (C) 2005 DeLano
Scientific LLC.
A current PyMOL Maintenance and/or Support Subscription may be required
for
legal usage of this Build beyond a finite honor-system evaluation
period.
Please visit http://www.pymol.org/funding.html for more information.
This PyMOL Executable Build is based on Open-Source PyMOL version 0.98.
OpenGL-based graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce2 MX/AGP/SSE/3DNOW!
GL_VERSION: 1.5.2 NVIDIA 66.29
Adapting to GeForce hardware...
coarsedim is [90.536896705627441, 101.45090210437775,
96.279500389099113]
finedim is [73.256998062133789, 79.677001237869263, 76.635000228881836]
center is [37.471499443054199, -27.388500571250916, 2.7424993515014648]
finegridpoints is [161, 161, 161]
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: 2 atoms did not have formal charges assigned
WARNING: 21 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 Apr 21 2005 at 18:02:41
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.
Valist_readPDB: Unable to parse resSeq token (E) 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!
--
Shiyong Liu 86-10-62757520
Wellcome to MDL sy...@mdl.ipc.pku.edu.cn
http://mdl.ipc.pku.edu.cn/~syliu
