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

Justin Lemkul jalemkul at vt.edu
Fri Aug 8 20:42:37 CEST 2014

On 8/8/14, 12:39 PM, Dawid das wrote:
> 2014-08-08 15:48 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>> The problem is in atom naming.  You have used MN1 and MC3 for the
>> equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes here,
>> because Phe-65 tries to make a bond to the +N atom, which it does not find
>> until it runs into Ser-69.  Likewise with the C atom in CH6.  If you rename
>> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.
> OK, I see your point but if I do as you suggest how will I specify
> nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
> atoms have different  vdW and electrostatic parameters than N and C atoms,
> respectively.

Realize that atom *names* and atom *types* are separate entities.  You have all 
your names and types the same, which can be confusing.  All you need to do is 
*name* the atom N and assign it a *type* of MNH1 or whatever it was.  Parameters 
are always assigned by type, not name.

>> If there are still missing parameters for interactions, you'll have to
>> figure that out.  There are several missing inter-residue angles and
>> dihedrals in your .rtp entry for CH6.
> Do you mean those which I stated above?

Above?  You mean in a previous message?  Most of those errors were derived from 
incorrect, nonsensical bonding.



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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