[gmx-users] New residue in FF does not bond to others.

Justin Lemkul 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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