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.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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 14 2004 - 15:53:06 PST
