Hi Michael, i have just updated to the latest version of apbs-0.3.2 and pymol-0.97 under debian linux and get the following error messages (see below) + a completely positively charged protein surface...
using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html' of the same protein works, so there seems to be a problem with the build-in generation of pqr-files. i tried 3 different proteins from the PDB with and w/o ligand and water atoms. any idea what's going wrong? cheers, Peter ------------------------------------------------------------------------------ PDB code 1ini all waters and ligand atoms removed by hand ... 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: 5 atoms did not have formal charges assigned WARNING: 10 atoms did not have properties assigned ... This executable compiled on Nov 22 2004 at 15:59:46 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 (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: Loading from 'pymol-generated.dx'. DXStrToMap: Dimensions: 129 129 97 DXStrToMap: Origin 14.554 -48.010 -7.484 DXStrToMap: Grid 0.579 0.523 0.664 DXStrToMap: 1614177 data points. ObjectMap: Map Read. Range = 3352.843994 to 12333.959961 ___________________________________________ Peter Haebel Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49-6421-28-28994 email: peter.hae...@staff.uni-marburg.de http://www.agklebe.de NAD3-Workshop 2005 - Divide&Conquer http://www.agklebe.de/workshop2005
