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

From: Pratul Agarwal <>
Date: Tue, 29 Jan 2019 14:18:12 +0000


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.


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 1/28/2019 12:15 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
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Received on Tue Jan 29 2019 - 06:30:03 PST
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