AMBER Archive (2003)

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

From: Dalmaris, John (john.dalmaris_at_imperial.ac.uk)
Date: Thu Dec 11 2003 - 12:01:35 CST

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David A. Case
Sent: 10 December 2003 16:34
To: amber_at_scripps.edu
Subject: Re: AMBER: xleap-N/C terminus

Hello Prof Case,

I have been trying altering the prep file for the amino acids on Xleap
putting the N atom (and its H) last and the C atom (and its O first). Upon
loading the new prep file on Xleap I get an error message: Atom CA: Illegal
chain specifier [H] in prep file. -M CA N H

I have reversed the order of the IMPROPER sequence but still the same
message. Does the IMPROPER specify whether CO or NH will be first connected
to the CA when reading the peptide from left to right? Is there any other
alteration that I have to do on the prep file?

Many thanks for the help.

Best wishes,

John

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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