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

From: mish <>
Date: Thu, 31 Jan 2019 13:07:56 +0000

Many thanks Dave. Yes, Shirts paper from 2003 was the first to do this and
then some other people also followed the same procedure. I did check those
papers but didn't find anything in more detail than this. But it is clear
enough and it should be possible by creating and editing lib/off files for
each residue.

I just thought to check if such files are already available somewhere as
GROMOS probably has something like that (I am not sure though!).


On Thu, Jan 31, 2019 at 12:46 PM David A Case <>

> 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
> it.
> 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 - 05:30:02 PST
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