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

Justin Lemkul jalemkul at vt.edu
Thu Jul 16 19:06:43 CEST 2015

On 7/16/15 12:57 PM, sridhar dwadasi wrote:
> Hi Dr. Justin Lemkul,
>        Thank you for responding again. I'm still not understanding it :(.
>   I'll try to be more clear. Taking the example of OPLS UA, we have
> different atom types for united alkene atoms (-CH= and CH2=) and alkanes
> (-CH2-). When I represent the connections in n2t file, the -CH2- and -CH=
> will have two connections each. and the distances with other united carbons
> are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the
> same information in the .n2t file. Based on the order in which they appear
> in the .n2t file, the atom appearing first is being taken by x2top to
> create the topology. I hope I made my problem clear. I'm unable to post my
> .n2t file now as I do not have it with me at the moment. If required I can
> post it tomorrow.

Yes, please post the .n2t file.  Just keep in mind that x2top is a very 
simplistic program; you may have to play some tricks to get such a subtle 
distinction to work correctly.  UA models will be particularly tricky because 
there won't necessarily be any H to distinguish different forms.  You may have 
to either play with the specified bond length (putting one outside of the 10% 
tolerance of the other) or re-compile the code after modifying the allowable 
tolerance.  In this case, 10% may be too permissive.



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


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