Hello
Did you prepare the Cys residues according to comply with zaff force field?
Here is the link
https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
On Tuesday, 14 September 2021, Debostuti Ghoshdastidar <
debostutighosh.gmail.com> wrote:
> Hello Everyone
>
> I am simulating a nuclear receptor protein which is known to coordinate
> zinc via 4 cysteine residues. I carried out a simulation of the crystal
> structure of this protein in complex with DNA. During
> minimization/equilibration I applied harmonic restraint and graded it off
> slowly from 20 to 5 kcal/mol before turning it off. The production run was
> carried out without any restraint.
>
> I applied restraint on all atoms of protein and DNA as well as the zinc as
> part of a single group:
> -----------------------------------------
> Restrain all the atoms
> 20.0
> RES 1 368
> END
> END
> --------------------------------------------
> While the output file shows that restraint has been applied on all atoms of
> the group, the ZN continues to remain dynamic in the system and escapes
> binding during the minimization/equilibration phase itself while being
> under restraint. The remaining protein/DNA obviously undergo hardly any
> changes while being under restraint.
>
> Could someone help me understand why this could be happening.
>
> Thank you
> --
> Debostuti Ghosh Dastidar
> Research Associate
> PDB-India
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--
Regards
Elvis
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Received on Tue Sep 14 2021 - 18:30:02 PDT
