On 3/27/15 4:05 AM, Priya Das wrote:
The following is the attached pose.str file. 1) Does param penalty or charge penalty matters?
Yes.
2) How do we know that the list does not accept attachments?
It's something I say weekly, if not more often. It should also have been in the welcome email when you subscribed.
3) I am following the tutorial for validation of penalties. As CHARMM is not free cannot download it. So using Accelry's Discovery Studio interface to perform QM-MM calculations (nstep= 500).
There is no QM/MM in the parametrization. There are QM calculations for bonded parameter scans, frequency calculations, and water interaction energies. Any MM or MD software that can do single-point energy evaluations and geometry optimizations can handle the MM energy part. CHARMM is just very easy to use in this case. You can certainly do the MM energy evaluations and optimizations in GROMACS or whatever software you like, though it may be a bit laborious.
-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 [email protected] | (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 [email protected].
