[gmx-users] Distance restraint and pull code
hongtham0709 at gmail.com
Fri May 27 03:20:34 CEST 2016
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
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.
even I tried to increase the fac from 0.1 to 10, but It didnt worked.
Can anybody help me?
Thank you so much.
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