Re: AMBER: prep file new residue

From: David A. Case <>
Date: Tue, 24 Apr 2007 12:12:44 -0700

On Mon, Apr 23, 2007, Dr M. Blomberg wrote:
> I want to do simulatons with Glutathione as a substrate, which is a
> tripeptide (QCG) with the Glu forming the peptide bond with it's sidechain
> carboxylic group.
> I have tried to change the connectivity tree, i.e. M, B, E etc, and
> creating a new residue prep file with the main chain going through the side
> chain. However, when I load the prep file into leap I get the error below
> and the new residue is not loaded. Could someone please tell me how to do
> this correctly?

Without knowing what you gave for the tree identifiers, it's not possible to
help very much.

But the easiest is probably just to read in a pdb file with the structure,
and use the bondbydistance command to get the bonds. Check visually that
things are OK, then save the output in prep or mol2 format.

...good luck...dac

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Received on Wed Apr 25 2007 - 06:07:35 PDT
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