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" <jalem...@vt.edu> 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 list gmx-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 list gmx-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
