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

[Justin Lemkul]

On 10/14/19 11:54 PM, ISHRAT JAHAN wrote:
> 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

Please update your bookmarks. That site is wildly outdated and will be 
taken offline soon.

Use the tutorial at http://www.mdtutorials.com/gmx/complex/index.html 
instead.

-Justin

> 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.
>>> --
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>>>
>>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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