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!