Re: [AMBER] Non-Standard Residues Problems

From: Ben Roberts <ben.roberts.geek.nz>
Date: Wed, 29 Jun 2011 13:50:25 -0400

Hi David,

On 29/6/2011, at 1:38 p.m., David Cantu wrote:

> Dear Amber Users/Developers,
>
> We have a protein, which has a phosphopantethiene group (call it resiude
> PPP) attached to a serine (through a P-O bond). We tried loading this
> Ser-PPP residue into antechamber, but failed.
>
> If we load the PPP by itself, using Antechamber, a hydrogen will take the
> place of the P-O bond. We cannot load it with an open valence. Any ideas no
> how to load both the PPP and Ser as a non-standard resiude? We need the
> correct parameters for the P-O bond.

About the only thing I can suggest is to combine the PPP and serine into a
single residue, with its own three-letter residue code and residue number. Then,
antechamber should handle it without any problems.

Good luck!

Ben

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Received on Wed Jun 29 2011 - 11:00:06 PDT
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