Re: [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx
I agree with Justin that the way to do this is by adding a new entry to the .rtp file. The only point I would make is that as you seem to be missing the gamma phosphate and its oxygens would it not make more sense to start from an ADP topology? Also you should ask (or have asked) yourself why these atoms are missing in your start structure and do they need to be added back or are they missing for a purpose. Tom --On Thursday, May 07, 2009 06:59:21 -0400 "Justin A. Lemkul" wrote: Una Bjarnadottir wrote: 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 The [ exclusions ] are pre-defined in the force field .rtp file. The easiest way I can see to get around this is to make a local copy of the .rtp file, make a new entry for your molecule based on the ATP entry (deleting out whatever atoms are not present) and trying again, using a new name for this partial ATP, in both the .rtp and .pdb files. The -missing option, as described by pdb2gmx is "dangerous" for this reason. -Justin How can I resolve this first not done by -missing command? Cheers, Una -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx
Una Bjarnadottir wrote: 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 The [ exclusions ] are pre-defined in the force field .rtp file. The easiest way I can see to get around this is to make a local copy of the .rtp file, make a new entry for your molecule based on the ATP entry (deleting out whatever atoms are not present) and trying again, using a new name for this partial ATP, in both the .rtp and .pdb files. The -missing option, as described by pdb2gmx is "dangerous" for this reason. -Justin How can I resolve this first not done by -missing command? Cheers, Una -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] atom name O3PB not found in residue ATP 340 while generating exclusions when running pdb2gmx
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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
