[gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx

[Una Bjarnadottir]

Dear all,

I'm running a simulation of a structure which has part of ATP bound to 
it so I'm using the -missing command when running pdb2gmx

pdb2gmx runs and lists the missing atoms and than it gives a fatal error 
about missing atom name!

WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
WARNING: atom APG is missing in residue ATP 340 in the pdb file
WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
         You might need to add atom H3PG to the hydrogen database of 
residue ATP
         in the file ff???.hdb (see the manual)

There were 17 missing atoms in molecule Protein_A
Number of bonds was 3730, now 3725
Generating angles, dihedrals and pairs...
Fatal error: atom name O3PB not found in residue ATP 340 while 
generating exclusions

How can I resolve this  first not done by -missing command?

Cheers, Una

-- 
Una Bjarnadottir           School of Biomolecular and Biomedical Science
Conway Institute           UCD
Dublin 4, Ireland          Phone: +353 1 716 6874, Fax: +353 1 716 6898
Email: Una.Bjarnadottir at ucd.ie