Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
Andy Somogyi wrote: Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types not present in Gromac's charm27. I looked into whatif, but unfortunately it's not free OSS. Wonder if I could use vmd's autopsf, and then write something that changes the atom types?? Any ideas? My favorite tool for simple sidechain rebuilding: http://spdbv.vital-it.ch/ It offers a rotamer library and the naming conforms to the normal standard so there are no issues when using the fixed files as input into pdb2gmx. -Justin Thanks On Mar 23, 2012, at 5:39 PM, "Justin A. Lemkul" wrote: Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file. Either the atom is named differently or it is missing. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? No. The contents of the input coordinate file must match what is expected by the .rtp file. If you have missing atoms, they must be modeled in using external software. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types not present in Gromac's charm27. I looked into whatif, but unfortunately it's not free OSS. Wonder if I could use vmd's autopsf, and then write something that changes the atom types?? Any ideas? Thanks On Mar 23, 2012, at 5:39 PM, "Justin A. Lemkul" wrote: > > > Andy Somogyi wrote: >> Hi All, >> I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, >> http://viperdb.scripps.edu/info_page.php?VDB=1dzl >> using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top >> I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: >> Fatal error: >> Atom CG is used in the topology database, but an atom of that >> name was not found in residue number 1. >> I have not have much luck finding this error in any mailing list. > > I've never seen that error before, but it sounds like there is an atom named > 'CG' in the .rtp entry but not in the coordinate file. Either the atom is > named differently or it is missing. > >> If the PDB does have missing atoms, can pdb2gmx guess missing atoms like >> VMD's psf gen? > > No. The contents of the input coordinate file must match what is expected by > the .rtp file. If you have missing atoms, they must be modeled in using > external software. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
On 2012-03-23 05:39:38PM -0400, Justin A. Lemkul wrote: > > > Andy Somogyi wrote: > > Hi All, > > > > I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, > > http://viperdb.scripps.edu/info_page.php?VDB=1dzl > > > > using > > > > pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top > > > > I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: > > > > Fatal error: > > Atom CG is used in the topology database, but an atom of that > > name was not found in residue number 1. > > > > I have not have much luck finding this error in any mailing list. > > > > I've never seen that error before, but it sounds like there is an atom named > 'CG' in the .rtp entry but not in the coordinate file. Either the atom is > named > differently or it is missing. > > > If the PDB does have missing atoms, can pdb2gmx guess missing atoms like > > VMD's psf gen? > > > > No. The contents of the input coordinate file must match what is expected by > the .rtp file. If you have missing atoms, they must be modeled in using > external software. I wonder if there is a way to overload the hydrogen-adding mechanism to add heavy atoms too. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file. Either the atom is named differently or it is missing. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? No. The contents of the input coordinate file must match what is expected by the .rtp file. If you have missing atoms, they must be modeled in using external software. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Fatal error: Atom CG is used in the topology database...
Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? Any ideas? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
