[gmx-users] distance restraints around Zn atom

[Priyanka Shah]

Dear all,

I want to apply distance restraint between Zn and its coordinating
atoms. Zn is supposed to be in octahedral geometry. Zn is making
coordination bond with O of hydroxyl group in ligand atom also. Even
after several attempts, it seems like destance restraint is not
effective because after 1ns MD run, ligand and Zn both move away from
their position in opposite directions.

 I have put following lines in mdp file:

title       = Protein-ligand complex
define      = -DPOSRESLIG   ; distance restrain from metal
disre = simple

and added following lines into .top file
; Include Position restraint file
#ifdef POSRESLIG
#include "metalposre.itp"
#endif

where metalporse.itp contains

  671 11637 1     3          1  0.09   0.192     0.29        1
  4059 11637 1     7          1   0.11   0.21    0.31        1
  4070 11637 1    10          1  0.096   0.196     0.296          1
  4071 11637 1    12          1  0.094   0.195    0.295       1
11637 11662 1    14          1   0.12   0.23    0.32       1

where 671 -> OD2 of Asp45, 4059 -> NE2 of Hid267, 4070 -> OD1 of
Asp268, 4071 -> OD2 of Asp268, 11637 -> Zn and 11662 -> O of Lig.

looking for suggestions.

Thank you

Priyanka Shah
Central Drug Research Institute
Lucknow, India
-- 
Let spontaneity guide you!