[gmx-users] parameter for repeating units with cgenff

gromacs query gromacsquery at gmail.com
Fri Dec 11 20:20:28 CET 2015

Hi Justin

Thanks for the explanation. Just few things.

1) When you say " Initial charge fitting would be done on a side chain ..."
you mean using some QM method? Which seems expensive and needs expertise
which I dont have.

2) Also, as you said assigning charges and types with analogy does this
mean I can hand pick types and charges looking (carefully) some residues
available with CHARMM and can directly use them? At the same time, then in
this case, I should satisfy the condition of overall integral charge. Am
just wondering in future if reviewer raises question :)

On Fri, Dec 11, 2015 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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