Thank you Dave for the answer.
I have already done QM calculation on ligand with Gaussian, obtaining bond length and angle values. I have some problem to determine the harmony force constant…
Do you suggest to manually insert these parameters in GAFF.dat file? Should I call my atom "b. B. Boron”?
Vincenzo D’Amore
PhD student
University of Naples "Federico II"
> Begin forwarded message:
>
> From: David Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Amber parameters for Boron atom
> Date: 19 January 2019 at 15:34:42 CET
> To: AMBER Mailing List <amber.ambermd.org>
> Reply-To: David Case <david.case.rutgers.edu>, AMBER Mailing List <amber.ambermd.org>
>
> On Thu, Jan 17, 2019, Vincenzo Maria D'Amore wrote:
>
>> I’m trying to set up a protein-ligand complex for MD in Amber. My ligand
>> has a Boron atom. I have already optimised geometry and calculated ESP
>> with Gaussian. DO you have any suggestion to parametric the ligand due to
>> the fact that neither GAFF neither Amber has Boron atom type?
>
> Not really. There is a somewhat recent discussion here:
>
> https://github.com/openforcefield/smarty/issues/139
>
> My personal opinion is that the complexity of boron chemistry will inhibit
> creation of general force fields. It makes a *lot* of difference what
> kind of boron environment is in your ligand.
>
> You might consider doing QM/MM for the ligand. You'd still have to invent
> dummy MM parameters for the ligand, but that is not nearly as onerous as
> trying to get the good ones you would want for an MM-only calculation.
>
> ....dac
>
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Received on Sat Jan 19 2019 - 10:30:02 PST
