[gmx-users] How does x2top recognize between alkane C and alkene C

[Justin Lemkul]

On 7/13/15 1:38 AM, sridhar dwadasi wrote:
> Dear gromac users,
> I'm using g_x2top (4.6.7 version), to generate a topology. The compound
> contains double bonds. I have a problem in setting correct topology.
> The C1 in both the cases -C1H=C2H2 and -C1H2- is being assigned the same
> type, though I'm mentioning different distances in the n2t file. This may
> be due to the small difference in distance (0.140 nm and 0.154 nm).
> Can anyone suggest a way to go about this?
>

Because 0.14 and 0.154 are exactly 10% apart (w.r.t. 0.140) so x2top can't 
distinguish between them based solely on bond length.  The bonded connectivity 
is different, though, in terms of C1 (bonded to 3 groups only) so that suggests 
your .n2t file isn't constructed correctly.  C1 in the alkane should have 4 
substitutents, two of which are H.  In the alkene, 3 substituents, with 1 H.

-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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