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.bjarnadot...@ucd.ie
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