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?

Cheers,
Ehsan

----- Original Message -----
From: "Justin Lemkul" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@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

-- 
==================================================

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==================================================
-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to