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

[Jorden Cabal]

Dear Amit,
Yes, you need to correct the atom number in the "zn.itp" file in your case.
>From your co-ordinate file, it is clear that in order to restrain Zn atom
you need to put restraint potential on atom number corresponding to Zn atom
which is 4265 in your case instead of 2220. I think this should fix the
problem in your case. Try it and let me know if the problem persists.
Thank you.

On Tue, Oct 22, 2019 at 1:12 PM Amit Jaiswal <amitjai20 at yandex.com> wrote:

> Dear Jorden,
>
> Thanks for your reply. As you have suggested, i found there is a mismatch
> of the atom number in the zn.itp file and the .gro file. I have included
> few residues of .gro file for your convenience.
>
> What i understand is that I have to rename the zn.itp file with residue
> no. 4265 and not 2220. Please correct me if I am wrong.
>
> And also you suggested me to "minimize the system very carefully". What do
> you mean by this? Should i use lesser minimisation steps ?
>
> Thanks for your time and efforts.
>
> With kind regards,
> Amit
>
> 391THR HG22 4260 4.897 5.356 3.136
> 391THR HG23 4261 4.889 5.247 2.993
> 391THR C 4262 4.600 5.071 3.244
> 391THR OT1 4263 4.599 5.012 3.355
> 391THR OT2 4264 4.496 5.082 3.173
> 392ZN ZN 4265 7.278 6.612 5.838
> 393NAD PA 4266 6.217 7.359 2.802
> 393NAD O1A 4267 6.090 7.410 2.863
> 393NAD O2A 4268 6.337 7.451 2.808
> 393NAD O5B 4269 6.185 7.331 2.647
> 393NAD C5B 4270 6.082 7.233 2.620
>
>
>
> 19.10.2019, 21:53, "Jorden Cabal" <jordencabal at gmail.com>:
>
> Dear Amit,
> Your files look correct to me. If "2220" atom in your coordinate file is
> the "Zn" atom, it should not be displaced because, from your mdp file and
> topology setting you have restrained all the heavy atoms of Protein, Nad
> and Zn. I don't understand why it is happening. Even the restraining force
> you are taking is good enough.
> I suggest you to check if the atom number 2220 in the co-ordinate file
> (.gro file) is Zn atom or not? If it is not then you have wrongly selected
> atom number for restraining. Also, if you are following the standard
> tutorial for energy minimization which do not restrain any atom, I suggest
> you to check the position of Zn atom in structure you get after energy
> minimization. If the location of Zn ion is changed during the EM, then you
> will need to minimize the system very carefully.
> Hope this will fix your issue.
> Thank you
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