Thread: [Apbs-users] problem with phosphoserine
Biomolecular electrostatics software
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From: Michel Espinoza-F. <me...@dd...> - 2005-05-06 02:05:03
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Hi all, =20 I was trying to get the electrostatic potential of some peptides containing phosphoserine employing the CHARMM ff parameters. I added the charges and radius to CHARMM.dat and successfully got the pqr files. The problem came up when I tried to submit my job; my job just crashed and I got the following: =20 Parsing input file pep1.in... Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from 1-25-p.pqr. Valist_readPDB: Unable to parse serial token (ATOM) as int! Valist_readPDB: Error while parsing serial! Valist_readPDB: Unable to parse resSeq token (SER) as int! Valist_readPDB: Error while parsing residue name! Valist_readPQR: Error parsing ATOM field! Error while reading molecule from 1-25-p.pqr Error reading molecules! =20 I was wondering if I need to recompile APBS using the modified .dat files containing the new parameters for the phosphate group. Is it true? I hope somebody could help me with this problem! Thank you. =20 Peace, Michel |
From: Todd D. <to...@cc...> - 2005-05-06 15:46:09
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Hi Michel - This sounds like a spacing issue - APBS is unable to handle chainIDs and columns that are merged together from PQR files. You might want to check for both of these cases, particularly problems like x/y/z coordinates bumping into one another due to large negative values. Alternatively, if you didn't use pdb2pqr (tools/conversion/pdb2pqr) to create your pqr file, pdb2pqr should be able to take care of the issues mentioned above. You can similarly edit the CHARMM.dat file contained there to add your parameters and the script should handle the rest. If either of these fixes don't work, feel free to send me your PQR file and I'll take a look. Todd Michel Espinoza-Fonseca wrote: > Hi all, > > > > I was trying to get the electrostatic potential of some peptides > containing phosphoserine employing the CHARMM ff parameters. I added the > charges and radius to CHARMM.dat and successfully got the pqr files. The > problem came up when I tried to submit my job; my job just crashed and I > got the following: > > > > Parsing input file pep1.in... > > Parsed input file. > > Got PQR paths for 1 molecules > > Reading PQR-format atom data from 1-25-p.pqr. > > Valist_readPDB: Unable to parse serial token (ATOM) as int! > > Valist_readPDB: Error while parsing serial! > > Valist_readPDB: Unable to parse resSeq token (SER) as int! > > Valist_readPDB: Error while parsing residue name! > > Valist_readPQR: Error parsing ATOM field! > > Error while reading molecule from 1-25-p.pqr > > Error reading molecules! > > > > I was wondering if I need to recompile APBS using the modified .dat > files containing the new parameters for the phosphate group. Is it true? > I hope somebody could help me with this problem! > > Thank you. > > > > Peace, > > Michel > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users |