----- Original Message ----- From: Sai Pooja <[email protected]> Date: Tuesday, October 26, 2010 7:26 Subject: [gmx-users] CT3 terminal To: Discussion list for GROMACS users <[email protected]>
> Hi, > > I use pdb2gmx command to convert a pdb file to a .gro and .top > file(using CHARMM forcefield). For the C terminus, I use the CT3 option which > is NCH3. When I use editconf to get a pdbfile from the .gro file generated, > the C=0 and the NCH3 seem to clash in space in pymol. It looks like Par has borrowed the mechanism for generating two carboxylate oxygens on a C atom (one each cis and trans wrt the third generating atom) for generating one amide nitrogen, and the code doesn't check which of cis and trans is already occupied by the carboxyl oxygen. Please file a Bugzilla so that this gets fixed. A real solution requires some coding, but you can get a crude work-around by replacing "1 8 NT C CA N" in share/top/charmm27.ff/aminoacids.c.tdb with "1 1 NT C CA O" See chapter 5 for details. This NT will be too close to carboxyl C, and EM will be needed to fix things. Mark
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
