On 11/6/14 8:38 AM, Venkat Reddy wrote:
Dear Justin, Yes, the problem is with the blank line at the end of atomtypes.atp. Now its working fine. I have added the missing dihedral types from other sources.
Thanks, I will fix that.
I have compared the cholesterol CHARMM parameters that are converted to gromacs format and original parameters from "toppar_all36_lipid_cholesterol.str" file available in CHARMM website. I found some variations in the atom types. For eg., The atom type of C3 atom from sterol ring in cholesterol is CTL1 in CHARMM whereas it is CG311 in charmm36-Nov2014.ff.
Which residue are you looking at? There is no C3 atom with type CTL1 in that stream file. In any case, CG311 and CTL1 have identical parameters (see ffnonbonded.itp) since CG311 is used for CGenFF model compounds, which in the case of lipids, were just ported over and given unique types. Anything with a "G" as the second letter in the atom type is from CGenFF, indicating "general" to differentiate them from the main CHARMM types.
-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.
