On 6/15/16 11:07 AM, Marlon Sidore wrote:
Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file clusters_ffbonded.itp, line 53]: Not enough parameters ERROR 2 [file clusters_ffbonded.itp, line 54]: Not enough parameters ERROR 3 [file clusters_ffbonded.itp, line 55]: Not enough parameters ERROR 4 [file clusters_ffbonded.itp, line 56]: Not enough parameters ERROR 5 [file clusters_ffbonded.itp, line 57]: Not enough parameters" The thing is, line 53 to 57 from this file is the dihedrals for one of the clusters: "SEHS FEHS SH CT 9 0.0 8,5772 3 FEHS SEHS FEHS SH 9 180.0 16,15024 5 SEHS FEHS NA CR 9 180.0 5,69024 3 SEHS FEHS NA CC 9 0.0 5,69024 3 FEHS SEHS FEHS NA 9 180.0 4,26768 5" I don't understand where there are missing parameters. Indeed, a classical line from the dihedrals of ffbonded.itp has the same number of parameters, for example: " C N CT C 9 180.0 1.44390 2 ; Amber03" Did any of you run into this before ?
Your force constants have commas. Use decimal points, otherwise they're not parsed correctly.
-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.
