Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true?

From: Bill Ross <>
Date: Sat, 24 Aug 2019 04:44:18 -0700

Boron as an ion in water will be parameterized differently than in a

   - in fact, nonbonded params will be different for each water model

   - charge will be integer +1..+3

Since you are comparing to Na, I'd assume you should have charge set to
+1, but since water doesn't 'see' it, I suspect you accidentally left it
as 0, since you didn't have to fit charge for a molecule.

/The dog did nothing in the night-time./

--Sherlock Holmes

On 8/24/19 4:18 AM, Erdem Yeler wrote:
> 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 (
> 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 - 05:00:02 PDT
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