On 6/17/16 4:42 AM, Anurag Dobhal wrote:
Dear Gromacs users, I want to simulate Guanine ( a nitrogenous base) molecules in water using OPLS AA force field. I used the "opls aa" parameters from atomtypes.atp ((JACS,113,2810(1991)). on calculating the total charge of one molecule it comes to a negative value.
The .atp file has no charges. The charges found in ffnonbonded.itp also mean nothing.
dose it means that guanine has negative charge ?
Not as just the base. The nucleotide form is of course anionic.
should I continue with thae same parameters or change them to bring the total charge of the molecule to zero.
You should be sure you have a proper model with a reliable source of parameters. Stripping the base out of a nucleotide also requires the introduction of an H to fill the valence at the glycosidic linkage. Charges may differ as a result of such a change.
-Justin
Thank You for your help *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai*
-- ================================================== 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.
