[gmx-users] double bond
esa38 at sfu.ca
Thu Oct 3 22:15:14 CEST 2013
Thanks Justin. I will try different bond parameters. I usually use PyMol or Chimera for visualization. Do you have any recommendation for a visualization software?
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, October 3, 2013 1:09:05 PM
Subject: Re: [gmx-users] double bond
On 10/3/13 3:08 PM, Ehsan Sadeghi wrote:
> Hi gromacs users,
> In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms.
> I added these commands in specbond.dat to resolve the issue
> NAF S 6 NAF O4 2 0.3 NAF NAF
> NAF S 6 NAF O5 2 0.3 NAF NAF
> But, it didn't solve my problem.
> Any suggestion for solving this problem?
There is no distinction between a single, double, or triple bond in an MM force
field, and Gromacs certainly doesn't change anything about the bonds. If your
desired geometry isn't being preserved, choose or derive better bonded
parameters. Also note that bonds will not break; visualization software often
guesses bonds incorrectly. What you see is not definitive. What is written in
the topology is.
Justin A. Lemkul, Ph.D.
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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