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 <jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.