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

From: Saikat Dutta chowdhury <>
Date: Tue, 14 May 2019 09:53:06 +0530

Respected Prof. Case,

Thank you for your suggestion.

With regards,

On Mon, May 13, 2019 at 6:22 PM David A Case <> wrote:

> 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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Saikat Dutta Chowdhury
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Received on Mon May 13 2019 - 21:30:02 PDT
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