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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Received on Tue Sep 14 2021 - 02:30:02 PDT
