[gmx-users] distance restraints around Zn atom

[Mark Abraham]

On 26/07/2012 3:27 PM, Priyanka Shah wrote:
> 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

Distance restraints and position restraints are totally different 
things. It looks like you need to clean up your work flow in this regard.

>
> 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.

Your .log and .edr files will have contributions from restraint 
violations, which you can use as a necessary-but-not-sufficient test for 
things working correctly.

Mark