[gmx-users] New residue in FF does not bond to others.
jalemkul at vt.edu
Wed Aug 6 20:54:10 CEST 2014
On 8/6/14, 12:04 PM, Dawid das wrote:
> Cause now what happens is that grompp requires bonding parameters for atoms
> which are actually bonded and for which are not (angle and dihedral
> parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want
> connection between Ser69-Phe65. Now grompp asks me about bonding paramters
> for atoms which build all three residues while these residues are separated
> by more than 4 atoms.
Properly constructed .rtp entries will not need manual editing, which is very
error-prone. You're using lots of strange atom names, so you need to establish
proper bonding from the CH6 residue; the +/- mechanism in flanking residues will
fail. If you're getting connections between non-consecutive residues, that
suggests a break in the chain when being processed by pdb2gmx; make sure CH6 is
defined as a Protein residue in residuetypes.dat.
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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