[gmx-users] parameter for repeating units with cgenff

gromacs query gromacsquery at gmail.com
Fri Dec 11 19:28:47 CET 2015

Hi Justin

I am bit lost I think. For e.g. in the amino acid residues library we have
-CO-CH(R)-NH- which we can combine these amino acids in any way and in the
rtp file it defines only these atoms and connecting atoms are mentioned

Now lets say I have some new amino acid -CO-CH(X)-NH- which I want to
combine with some existing amino acids. If I want to derive charges from
Cgenff what kind of residue I should prepare?
Is it NH2-CO-CH(X)-NH-COOH or may be CH3-NH-CO-CH(X)-NH-COCH3. But
ultimately I will be requiring only -CO-CH(X)-NH- part. So not considering
charges for the caps in topology will give non-integral charge or in other
words this part -CO-CH(X)-NH- will always be non-integral. Sorry am


On Fri, Dec 11, 2015 at 5:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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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