Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid

From: David A Case <>
Date: Mon, 13 May 2019 08:51:38 -0400

On Sun, May 12, 2019, Saikat Dutta chowdhury wrote:

>I am trying to simulate a homopolypeptide in explicit solvent condition.
>But the amino acid is phosphoglutamate, and I haven't found any parameters
>for this. Hence I tried antechamber for getting the parameters. I had built
>my polypeptide in Avogadro and followed the "Antechamber Tutorial" to get
>the parameters.

Antechamber is designed to create parameters for a single residue or
small molecule, not for polymers. What you want to do is to create a
single amino acid residue: the general procedure for doing this is
outlined in the "green fluorescent protein" tutorial. In brief, you
need to "cap" your desired residue with functional groups, so that you
have a chemically complete molecule. Then run antechamber, and later
remove the capping groups.

(I'm cc-ing this to Junmei, since my understanding was that his group had
simplified procedures for this.)

...hope this helps...dac

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Received on Mon May 13 2019 - 06:00:08 PDT
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