[AMBER] Metal ion parameterization using MCPB.py

From: Abhilash J <md.scfbio.gmail.com>
Date: Sat, 9 Nov 2019 13:42:25 -0500

 Hi Everyone,

    I am trying to generate AMBER parameters for a protein with MG and 4
water molecules using MCPB.py. The problem is the force constant is coming
out to be zero with one of the water molecules.
    I have tried to change the geometry slightly some times but all results
give the same result of zero force constant. I know the structure will be
octahedral from the crystal structure hence starting structure seems legit.
    I am using AMBER 18 with Gaussian. MG is bound by a ligand (ATP), 4
water molecules and a serine residue.
    Any help will be greatly appreciated.


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Received on Sat Nov 09 2019 - 11:00:02 PST
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