Dear Sir,
We want to do the force field parameterization for Zn metal in a
metalloprotease. A glutamate residue is essential to abstract the proton
from the ligand and hence facilitate the binding of the ligand with the Zn
ion in the active site. But we have to set a radius of 5.5 Å in the MCPB.py
input file to create the gaussian files containing glutamate residue as
well. But this results in extra coordination bonds between Zn and the other
atoms in the active site which we don't want.
We tried calculations with 2.8 Å and 5.5 Å in the MCPB.py input file. For
the calculations with 5.5 Å, we manually deleted /edited the non-standard
coordinations from *standard. fingerprint, *mcpbpy.frcmod, and the input
file for tleap. We could complete a 100 ns molecular dynamics simulation in
Gromacs with a parametrized force field. But we are not sure if this is the
correct procedure to address this issue.
When we calculated the MMPBSA binding energy using gmx_MMPBSA we got a
value of -52 kcal/mol for the MD calculations performed with 2.8 Å and -35
kcal/mol for 5.5 Å calculation. Further, the decomposition analysis gave a
positive contribution for the Zn ion in 5.5 Å calculation.
Could you kindly guide us to do the MCPB force field parameterization
calculations including the glutamate residue.
With thanks and regards
--
Shahid P
Research Scholar
School Of Biotechnology
National Institute of Technology, Calicut
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 17 2023 - 05:30:03 PDT
