On 5/13/16 5:04 AM, zeineb SI CHAIB wrote:
@ Justin Dear Justin, Thank you very much for the website. I tried to generate my topology from the website. After many problems in my input file, it finally generated the .str file with no error/warnings found but unfortunately some penalties were not good at all (> 50 and between 10 and 50)! How can I fix the file? 'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str'
You'll need to manually parametrize/refine anything that has bad penalties. Spend some time with the CGenFF paper and tutorial: http://dogmans.umaryland.edu/~kenno/cgenff/download.php http://www.cecam.org/upload/files/file_1187.pdf -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.
