The following is the attached pose.str file. 1) Does param penalty or charge penalty matters? 2) How do we know that the list does not accept attachments? 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).
Am i on the right track? On Mon, Mar 23, 2015 at 8:34 AM, Justin Lemkul <[email protected]> wrote: > > > On 3/22/15 12:37 PM, Priya Das wrote: > >> Dear all, >> >> I tried to generate parameters for ligand. I am not well in analyzing the >> penalty. >> Seeking advices if i need to further refine the parameters of the attached >> .str file to reduce the penalty. >> >> >> > The list doesn't accept attachments (if I had a nickel for every time I've > said that...) > > Penalties are described in the ParamChem FAQ, along with a link to the > CGenFF tutorial and paper. That's where you need to get your information. > > https://cgenff.paramchem.org/commonFiles/faq.php#validopt > > -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]. > -- *Let us all join hands to save our " Mother Earth"* ------------------------------------------------------------------------ Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala
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