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

[ISHRAT JAHAN]

Go through at the following link. Hope it will resolve the issue-
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html

On Tue, Oct 15, 2019 at 7:26 AM Jorden Cabal <jordencabal at gmail.com> wrote:

> 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.
> > --
> > Gromacs Users mailing list
> >
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh