AMBER Archive (2007)

Subject: Re: AMBER: (no subject)

From: David A. Case (case_at_scripps.edu)
Date: Thu May 10 2007 - 15:37:21 CDT

On Wed, May 09, 2007, Dingguo Xu wrote:

> I want to build a single amino acid using leap, for example ARG. And
> clearly, this residue has both N-term and C-term. But leap seems only
> recognize C-term. How to build both N-term and C-term for this single
> amino acid?

Antechamber is probably the most straigtforward approach: just create a pdb
file with the appropriate structure, and go from there. You might want to
consider using resp/RED for the charges, but that depends on what you plan
to do with this residue once you have created it.

...regards...dac

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