AMBER Archive (2006)

Subject: Re: AMBER: problem with prepfile

From: David A. Case (case_at_scripps.edu)
Date: Wed May 24 2006 - 15:56:08 CDT

On Wed, May 24, 2006, Shafinaz wrote:
>
> I have a problem during the generation of the prepfile of the molecule I
> would like to use. It is a steroid linked with a peptide.I tried many ways
> but could not solve that problem.

To help people understand your question, you should indicate what commands you
used, (just saying "I tried many ways" is not all that helpful), and what
"that problem" is.

Amber requires atom names within a residue to be unique. It looks like you
are trying to create a single residue with about about 16 amino acid residues
in addition to the steoid. Hence you have multiple atoms all named "N", etc.

You should have one residue that has just the modified single peptide, then
use LEaP to link that to other amino acids as you would for a protein. See
the instructions here:

    http://amber.scripps.edu/antechamber/example.html

for an example of how to create a non-standard amino acid residue.

...good luck...dac

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