AMBER Archive (2003)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Dec 10 2003 - 12:14:06 CST

> > 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.

I'm not sure I understand - is this a chemical or notational
difference? If notational, I would just write a small program
to reverse the order of residues in a pdb file.

Bill Ross

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