Hi I am a phd student and my advisor gave me "boron amber force field
parameterization" as my phd thesis. After 4 month, I finished all
parameterizations (nonbond and bond, angle, dihedrals (with paramfit), ESP
charges exc..). And Also I tested al parameters as gaff article did. My
parameters seemed quite good! Then he called me and said "I want to test
your parameters myself" and I went to his office.He opened linux system
computer and started simulation as tutorial B1 (
http://ambermd.org/tutorials/basic/tutorial1/section2.htm) and then he
said, "Look look water molecules are not adhering to boron atom so your
non-bond parameters are wrong" and he added "when I tried this with Na
(Sodium) atoms, water molecules adheres to Na atoms, your parameters
absolutely wrong". Actually, I got non-bond parameters from OPLC force
field and more than 88 articles did the same thing. I couldn't understand
what he said. My question is: Is my advisor's "approach" true? (I asked him
which article he saw this test he didn't answer ) and if it is true and
OPLS parameters "wrong" what can I do?
Thank you soo much
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Received on Sat Aug 24 2019 - 04:30:01 PDT
