[gmx-users] double bond

Ehsan Sadeghi 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.
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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