Hi Justin Thanks it worked, just to add I have to use -ignh as well. I think it does not detect some H at 5 end built from AMBER NAB programme.
Jiom On Wed, Feb 5, 2014 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/5/14, 9:49 AM, gromacs query wrote: > >> Hi All >> >> I have simple DNA pdb which has just 5 DA residues built from NAB in >> AMBER. >> I am trying to use pdb2gmx with charmm36-jan2014.ff downloaded from: >> >> http://mackerell.umaryland.edu/CHARMM_ff_params.html >> >> >> pdb2gmx -f a.pdb -o gro.pdb -ff charmm36-jan2014 >> >> >> I have changed all names according to DA residue defined in >> charmm36-jan2014.ff/merged.rtp but still I get error: >> >> Fatal error: >> atom N not found in buiding block 1DA while combining tdb and rtp >> >> > Use -ter to specify the appropriate termini. An unfortunate consequence > of our approach is that the protein and DNA termini are in one file. We > are looking at implementing a more generalized solution, but it won't be > for a while that we actually get to it. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.