[gmx-users] forcefield error for atoms

[Justin Lemkul]

On 3/26/15 5:04 AM, mah maz wrote:
> Hi Justin,
> Thank you! I checked the coordinates and I think there's nothing wrong with
> them. The problem might be from the .n2t file. I have some atoms without
> any bonds to other atoms in my system. So, in the .n2t file I assign 0 for
> bonds to other atoms. And it again stops with the same error while making
> the topology file. How can I get rid of this error?

You shouldn't be specifying anything with zero bonds in a CNT system.  That 
makes no sense.  You'll have to provide explicit detail of everything you're 
doing, including the contents of the .n2t file.  For a normal CNT, you only need 
one line, as there are only C atoms and they should all be equally spaced.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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