[gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Dear Amit,
During equilibration you add positional restraint for protein, notice that
you have added positional restraint for Zn ion, nad and protein. It should
not happen if you have taken the default values while generating the
positional restraints in gromacs. However I would like to look to your
"nvt.mdp",  "posre_zn.itp" and "posre_nad.itp" files, in order to comment
on it.

Thank you

On Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal <amitjai20 at yandex.com> wrote:

> Dear  Jorden,
>
> Many thanks for your suggestions. I solved the index file problem as I
> created two groups namely Protein_Zn_NAD and the other being Na_Water. But
> when i ran NVT equilibration, the Zn ion again got displaced far away from
> its original position. I cannot figure out how can i constrain the Zn ion?
> I guess something is wrong in the topology file. I have included the last
> few lines of my topology file. Please have a look whenever you are free and
> correct me if something is mistakenly wrong. Thanks for your time and help.
>
>
> *; Include Position restraint file*
> *#ifdef POSRES*
> *#include "posre.itp"*
> *#endif*
>
> *; Include Position restraint file*
> *#ifdef POSRES*
> *#include "posre_zn.itp"*
> *#endif*
>
> *; Include ligand topology*
> *#include "nad.itp"*
>
> *; Ligand position restraints*
> *#ifdef POSRES_LIG*
> *#include "posre_nad.itp"*
> *#endif*
>
> *; Include water topology*
> *#include "./charmm36-mar2019.ff/tip3p.itp"*
>
> *#ifdef POSRES_WATER*
> *; Position restraint for each water oxygen*
> *[ position_restraints ]*
> *; i funct fcx fcy fcz*
> *1 1 1000 1000 1000*
> *#endif*
>
> *; Include topology for ions*
> *#include "./charmm36-mar2019.ff/ions.itp"*
>
>
> *[ system ]*
> *; Name*
> *Protein in water*
>
> *[ molecules ]*
> *; Compound #mols*
> *Protein_chain_A 1*
> *ZN 1*
> *NAD 1*
> *SOL 12908*
> *NA 4*
>
> With kind regards,
> Amit
>
> 11.10.2019, 18:10, "Jorden Cabal" <jordencabal at gmail.com>:
>
> Dear Amit,
> Please check if the Zn ion is included in both the groups declared for
> temperature coupling. If you notice that it is is included, you can simply
> create a group of all the atoms which is not in "Protein_NAD" group. You
> can do this by using "!group_number" as far as I remember. Then try this,
> it should work. Please mail if the problem persists.
> Thank you and all the best.
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