[gmx-users] force field problem....

Ming Tang m21.tang at qut.edu.au
Thu Apr 16 15:09:52 CEST 2015

Hi, Justin
Thank you so much. I should be much more cautious in the future.
there is another interesting thing. why doesn't it give the warning regarding mismatching between CLA and CL when I use MG in the pdb and topol file?
I did not copy CN88. actually, I typed it. I got those 2 parameters from oplsaa. I found that in ffnanonbonded.itp in charmm27.ff, MG and CAL in different types of pairs has the same sigma1-4 and epsilon 1-4, so I give SR the same as well.

Sent from my Huawei Mobile

Justin Lemkul <jalemkul at vt.edu> wrote:

On 4/16/15 7:12 AM, Kamalesh Roy wrote:
> Dear all,
> please suggest for the topology for oleic acid..
> The information retreived after we run editconf...
> as a result atoms of the molecule becoming non bonded......in the box..

editconf doesn't add or remove bonds.  What you see in VMD (or whatever) is not
necessarily true (only the topology is definitive), but if the geometry is bad
then you'll get weird-looking states.  Your input coordinates could be messed up

> 8 out of 8 lines of specbond.dat converted successfully
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 1 residues with 20 atoms
> Making bonds...
> No bonds
> Generating angles, dihedrals and pairs...
> Making cmap torsions...There are    0 dihedrals,    0 impropers,    0 angles
>               0 pairs,        0 bonds and     0 virtual sites

Your .rtp entry is faulty if this is the outcome.


> Total mass 279.445 a.m.u.
> Total charge -1.000 e
> Writing topology
> Back Off! I just backed up oleic1.itp to ./#oleic1.itp.1#


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

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