On 7/22/15 1:00 PM, prasun kumar wrote:
Dear Justin and tarak Thanx alot for the reply If I have base atoms, so I have stacking information also. I was curious to know whether by changing the forcefield information will help me or not. For example, when I need ADNA, I will use some other information related to it and like that it continues for BDNA or ARNA
Any force field that needs to use conformation-specific parameters to enforce some geometry is a bad force field. Thankfully, I know of no force fields that do this. Proper force fields will correctly sample conformational fluctuations that reflect the real ensemble of the biomolecule in solution.
-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.
