On 3/28/15 7:05 AM, Priya Das wrote:
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> .
That file is not accessible. I'm not sure why there are high penalties in that molecule; it is very straightforward.
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.
Because neither CHARMM nor fftk do what you need to do. You need QM software that is capable of doing geometry optimizations, angle and dihedral scans, and vibrational analysis. We use Gaussian. If you don't have access to that kind of software, you're not going to be able to generate the target data you need, simply put.
On the MM side, assuming you can generate the QM target data for refinement, any package will work - CHARMM, GROMACS, etc. You don't explicitly need CHARMM. You need something that can do energy minimization and single-point energy evaluations.
-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].
