Hi Justin Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5 replaced by D* and D*3 by D* otherwise it ends with errors as said previously.
thanks JIom On Tue, Mar 4, 2014 at 1:00 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/3/14, 7:57 PM, gromacs query wrote: > >> Hi All >> >> Its in continuation. I am confused about something. In PDB file obtained >> from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them. >> PDB has DC5 as starting and DT3 as end residue and I get this error: >> >> pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or >> without >> -ignh) >> >> WARNING: atom H3' is missing in residue DC5 1 in the pdb file >> >> You might need to add atom H3' to the hydrogen database of >> building block DC5 >> >> in the file merged.hdb (see the manual) >> >> >> >> WARNING: atom H5'1 is missing in residue DT3 10 in the pdb file >> >> You might need to add atom H5'1 to the hydrogen database of >> building block DT3 >> >> in the file merged.hdb (see the manual) >> >> >> >> I found DC5 and others (D*5 and D*3) are missing in merged.hdb. Are these >> missing or intentionally not added? Also if I change name of DC5 to DC and >> DT3 to DT it works fine and all Hs are added without error. >> >> > Specific naming of terminal residues like this is not needed for CHARMM. > Just choose the correct termini (5TER and 3TER) and they will be patched > appropriately. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA 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.