[gmx-users] forcefield error for atoms

[Justin Lemkul]

On 3/24/15 10:30 AM, mah maz wrote:
> Hi Justin,
> Thanks for your reply. As you guessed correctly, for making a topology file
> I used "g_x2top -f  file.gro -o file.top -ff forcefield -noparam". I have a
> CNT system and I thought I should use g_x2top instead of pdb2gmx command.
> If I'm right, what may cause this error and what would be the solution?

Either the input coordinates are not suitable for constructing the topology, or 
the .n2t file is constructed incorrectly.  The fact that g_x2top found atoms 
with zero bonds indicates that some atoms are outside all possible distance 
criteria, hence zero bonds.

-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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