[gmx-users] Distance restraint and pull code

Justin Lemkul jalemkul at vt.edu
Fri May 27 17:10:58 CEST 2016



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


More information about the gromacs.org_gmx-users mailing list