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

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