[gmx-users] Mix NVT and NVE
Hi All Is it possible to have to fix the temperature of one subsystem, but leave the other parts alone? Say for example you have protein and solvent, so what would happen if you only have a single tc_grps = SOL and leave Protein alone. Reason I ask is I would like to look at the time dependent exchange of energy with a solvent fixed at a temperature, and some proteins in contact with this solvent -- so energy would only be exchanged at the boundaries of the protein - solvent. 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
[gmx-users] CMAP in Gromacs Vs. CHARMM
Hi, I'm trying to figure out the differences between Gromacs and CHARMM implementation of CMAP. In Gromacs it seems to be defined as a 5 body term, whereas in CHARMM, its a 8 body term. I thought CMAP was a correction between a pair of dihedrals, 4 atoms define a dihedral, so I'm not sure how the .top format can specify this relationship using only 5 atoms. Could anyone shed some light on converting between them. 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
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
[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
