On 5/26/16 9:20 PM, HongTham wrote:
Dear Gromacs users, Im running a Zn bound protein - ligand complex system. Zn makes coordinations with 3 HIS and NH- of ligand. in the itp file, Zn and protein in the same [molecule] but not ligand. because it cant be applied distance restraint ZN and ligand (they are belong to different [molecule]), I applied distance restraint for ZN and 3 HIS, and used pull code to keep ligand closed to ZN This is the distance restrains assigment in topology file of ZN and protein, while 3852 is ZN and other is HIS atoms. [ distance_restraints ] ; ai aj type index type low up1 up2 fac 3852 1354 1 0 1 0.2 0.21 0.22 0.1 3852 1390 1 0 1 0.2 0.21 0.22 0.1 3852 1721 1 0 1 0.2 0.21 0.22 0.1 The pull code in mdp file is like below, in which, a_3862 is N atom of ligand disre = simple ; distance restraints disre_fc = 1000 ; Force constant pull = umbrella pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = ZN pull-group2-name = a_3862 pull-geometry = distance ; simple distance increase pull-coord1-groups = 1 2 pull-dim = Y Y Y pull-coord1-rate = 0.0 ; not pull, just distance restraint at a reference distance bw 2 groups pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 pull-start = yes ; define initial COM distance > 0 pull-nstxout = 5000 pull-nstfout = 5000 It seemed the pull code worked well. The problem is the distance restraint is not effective. ZN only can be kept closed to one of three HIS, and moves far away from 2 others.
Because you defined one restraint using the pull code. Either define multiple restraints or increase the strength of your distance restraints.
-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.