AMBER Archive (2003)

Subject: Re: AMBER: xleap-N/C terminus

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 10 2003 - 10:33:52 CST

On Wed, Dec 10, 2003, John wrote:
>
> Xleap designs peptides with the N-terminus on the left and the C-terminus on
> the right. I want to reverse such a peptide so that I can have the
> C-terminus on the left in order to get this residue as residue No 1 in my
> pdb file. I have tried creating this peptide in ChemDraw but when I load it
> on Xleap it keeps connecting the C=O of residue i with the N-H of residue
> i+1. Is there anyway in Xleap to do it the other way round and connect NH of
> residue i with the CO of residue i+1?
>

You have to re-organize your prep files so that the first main chain atom is
C and the last main-chain atom is N. Or, edit an off (aka "lib") file, and
swap the connect1 and connect2 values. This should turn around the sense of
the chain progression.

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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