[gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/11/15 1:28 PM, gromacs query wrote:
> 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
> specifically.
>
> 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
> confused.
>

The backbone group always has a charge of zero, so you only deal with the side 
chain when deriving charges.

Initial charge fitting would be done on a side chain analog that terminates in a 
-CH3 that is analogous to CB.  Once that work is done, the model compound is 
merged with the backbone and CB (which is -CH2, so generally the third H charge 
is just lumped into the C charge) and torsional fitting is done for 
chi1/chi2/etc using a dipeptide model of the amino acid.  But at that point the 
charges are done.

I also wouldn't use CGenFF for a modified amino acid; derive parameters by 
analogy from the parent CHARMM force field.  CGenFF is generalized, at the 
expense of some accuracy.  Mixing CGenFF into a polypeptide chain is not the 
most robust approach.  CHARMM has excellent coverage for most chemical moieties. 
  Simply assigning charges and types by analogy should be quite straightforward.

-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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