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

[Justin Lemkul]

On 10/22/19 12:04 AM, Amit Jaiswal 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.

The global atom number is irrelevant in defining position restraints 
(and will actually trigger a warning in your case). If Zn is defined as 
a separate [moleculetype] in its own .itp file, the only valid atom 
number for position restraints is 1. See 
http://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds

-Justin

> 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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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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