[gmx-users] parameter for repeating units with cgenff

Justin Lemkul jalemkul at vt.edu
Fri Dec 11 18:50:18 CET 2015

On 12/11/15 12:17 PM, gromacs query wrote:
> Hi Justin
> Thanks for the reply. Yes your are right and indeed, sorry I forgot to
> mention, I tried with some CH3 and other groups which may be considered as
> an appropriate 'cap' which is normally followed by many. But in this case I
> will have to remove the cap e.g. B-O-CH3 to B-O- before joining to the next
> residue. This causes a net non-integral charge on B-O- which is not correct
> as disturbs overall integral charge of the polymer. Ideally the cap once
> removed should leave B-O with integral charge. I have tried many caps but
> none of them after being removed leave B-O to be integral.

Capping groups can't simply be chopped off; that will naturally lead to a 
useless topology.  They need to be designed such that their parameters (charges, 
etc) are analogous to the full-length species such that they can be merged with 
flanking groups.



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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