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After I ran 1AHO through PDB2PQR, I found 4 atoms where the atom and
residue names had "collided": atoms 178 and 179 of CYS 12 and atoms 944
and 945 of CYS 63. This appears to be due to the insertion of "A" and "B"
after the atom IDs to indicate multiple conformers (I think). In fact,
this problem also appears with other residues in the protein but PDB2PQR
didn't appear to do anything with it...
We'll think about ways in which to make PDB2PQR more robust to these types
of entries in the PDB. In the meantime, I'd recommend hand-editing the
PDB file before submission to PDB2PQR to manually select the conformers
--- Douglas McKinney <lycius_down@...> wrote:
> I used PDB2PQR to convert 1AHO.pdb to a pqr file. I
> also used the generated apbs input file from the
> PDB2PQR server. I am receiving the same error a
> previous person has had posted
> I followed the advice but I still received the error
> after looking over the generated pqr file. I observed
> no flaws, or columns running into each other. 1aho.pdb
> is not the only file this has happened to either. Is
> there a remedy?
> > Parsing input file 1aho.in...
> > Parsed input file.
> > Got PQR paths for 1 molecules
> > Reading PQR-format atom data from 1aho.pqr.
> > Valist_readPDB: Unable to parse serial token (ATOM)
> as int!
> > Valist_readPQR: Error parsing ATOM field!
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Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Washington University in St. Louis