Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues

From: David A Case <>
Date: Thu, 31 Jan 2019 07:46:22 -0500

On Thu, Jan 31, 2019, mish wrote:

>I thought it makes sense to
>keep the side-chain part exactly same as in AMBER14 force-field and just to
>change it on Cb. This is going to affect some properties but the
>interaction of side-chain part with my small molecules may not be affected
>much and I can still keep parameters closer to native AMBER force-field.

I agree with the above. Among other things, there are lots of
calculations out there that have used exactly this scheme. (I think
Michael Shirts was the first to do this, but I'm not sure.) Certainly,
if you plan to draw some conclusions about the Amber14SB force field,
this seems like the best way to proceed. (At least to me.) Since there
are only 19 amino acid sidechains, it wouldn't take very long to just do

OR, check the supplementary materials in the literature. People that
have carried out these sorts of calculations are quite diligent in
providing complete details of what they have done. So there might be
some files out there. The relevent authors are probably not following
the Amber mailing list. Try an email to Michael or David Mobely.

...good luck...dac

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Received on Thu Jan 31 2019 - 05:00:01 PST
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