[gmx-users] New residue in FF does not bond to others.
addiw7 at googlemail.com
Wed Aug 6 20:57:59 CEST 2014
Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to
work it out then?
2014-08-06 19:45 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> On 8/6/14, 12:04 PM, Dawid das wrote:
>> Cause now what happens is that grompp requires bonding parameters for
>> 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
>> 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
> 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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