I have also carried out MD simulation for the same comlex in water and that worked perfectly.
On Thu, Oct 16, 2014 at 1:50 AM, Justin Lemkul <jalem...@vt.edu> wrote: > [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible > for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule > <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3Dcn7kjseE1qsZ3%252Fyd7n0%252FnivMrWPikx9abmED9c1Z42zTxtJsdJ4Nlq8B1dPjg96fP9AJ16aIbU8Kj7OnCGkj2WcFizgzmQOxfGDp41XzFi%252FbKCndwpcMOGrzAQcBkfgtR1XTfCbCQOE%253D%26key%3DO1Af6fqB%252BADty4CrThw297lFG47eK14mpIp97%252FGkvi0%253D&tc_serial=18958403331&tc_rand=66307849&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001> > | More info > <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=18958403331&tc_rand=66307849&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001> > > > > On 10/15/14 12:35 PM, Padmani Sandhu wrote: > >> Hello Justin, >> >> >> >> Epot = -3.4264112e+07 >> Fmax= 8.5767386e+02 >> from energy minimization. >> >> > Seems reasonable. > > I am using force field Gromos43a1 and ligand parameters were derived from >> PRODRG. >> > > PRODRG produces topologies full of errors. Have you done any manual > adjustments to improve the quality of the topology? > > I have also minimized same protein-ligand complex in the water ealier. >> >> > So minimization works, but does an MD simulation work? That will help > sort out whether or not the issue is related to the membrane. > > -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. > > -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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.