Thanks a lot ... I feel really dumb here ~~ Marlon Sidore
PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-15 17:26 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > 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. > -- 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.
