[gmx-users] Termini database-more details , meaning of each lines and how to add or delete atoms-reg
jalemkul at vt.edu
Sat Aug 15 19:36:17 CEST 2015
On 8/15/15 1:32 PM, Nikhil Maroli wrote:
> how to add and delete atoms and meaning of each lines in both
> aminoacids.n.tdb and aminoacid.c.tdb
Read the manual, section 5.6.5 where everything is explained.
> My structure is cyclic peptide rings i have to remove Oxygen from -COO end
> Hydrogen from -NH3 end of the first and last amino acids..
This doesn't require .tdb modification. Choose 'None' for the termini and
either use specbond.dat to complete the cyclization or manually add the bonded
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
More information about the gromacs.org_gmx-users