I am sorry to bother again and again. I am new to it and still learning the basics. My molecule is a decahydroquinoline. The paramchem generated .str file is HERE <https://cgenff.paramchem.org/initguess/filedownload.php?file=20150328/Pose1.str> . I am following CGennFF tutorial and your instructions as HERE <http://mackerell.umaryland.edu/~kenno/cgenff/program.html>. As penalties are there i need to use QM, but i am not able to run CHARMM simulations as CHARMM is not freely available. So tried to use this Toolkit <http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/>, but still in vain.
On Fri, Mar 27, 2015 at 4:52 PM, Justin Lemkul <[email protected]> wrote: > > > 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]. > -- *Let us all join hands to save our " Mother Earth"* ------------------------------------------------------------------------ Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- 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].
