AMBER Archive (2003)

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

From: Jiten (jiten_at_postech.ac.kr)
Date: Wed Dec 10 2003 - 07:10:15 CST

Hai John,

I hope you could remove the un-desired bond and connect the desired bond
using the Xleap. How good are the xyz coordinate generated by the ChemDraw -
you cound istead directly draw inside the Xleap.

I hope this helps,

Jiten
----- Original Message -----
From: "John" <john.dalmaris_at_imperial.ac.uk>
To: <amber_at_scripps.edu>
Sent: Wednesday, December 10, 2003 9:34 PM
Subject: AMBER: xleap-N/C terminus

> Hello Amber users,
>
> 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?
>
> Many thanks in advance.
>
> Best wishes,
>
> John
>
>
>
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