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.