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

From: mish <>
Date: Thu, 31 Jan 2019 12:00:29 +0000

Thanks a lot for the suggestion. The latest paper I saw was from 2006 or
2007, so, yes a bit old.

Calculating RESP charges look systematic but I was just afraid about the
change of charge in protein-side chain part. 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.
Cased where small molecule will be interacting closely to Cb will
definitely need some attention!

I just felt that I have fewer emails from Amber mailing list in the last
few days and then check the archive. For some reasons, I didn't receive
Pratul's response to my query but there was one in archive:

Are the papers you found recent? The approach of manual adjustment of
charges was common more than a decade ago, when it was computing intensive
to compute charges. Now, you can use Antechamber. It may also not be a bad
idea to use "resp" to calculate the charges, one could argue that this
would be a more systematic way.


On Mon, Jan 28, 2019 at 5:15 PM mish <> wrote:

> Dear all,
> I am looking for suggestion to construct amino-acid side chain analogues
> in Amber. I found a number of papers describing the charge adjustment (
> adding hydrogen to Cb whose charge is same as the other hydrogen attached
> to Cb, and then adjusting the charge of Cb to ensure net integral charge).
> I am curious if such parameters are already available somewhere or if
> there is any quick way to do it in tleap/parmed.
> Our plan is to compute the affinity of certain compounds towards
> amino-acid side chains.
> Best Regards
> Mish
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Received on Thu Jan 31 2019 - 04:30:01 PST
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