AMBER Archive (2003)

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

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Wed Dec 10 2003 - 09:46:22 CST

Hello Jiten,

Yes, I have tried to manually alter the bond connectivity. I erase the amide
bond between the CO (of residue i) and NH (of residue i+1) and manually
connect the NH (of residue i) to the CO (of residue i+1). Xleap does not
recognise this connectivity and when check the pdb file each residue is
treated as separate unit (TER after the end of each residue). When load pdb
file on Xleap again it connects the units in the CO(i)NH(i+1) fashion.

Thanks,

John

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Jiten
Sent: 10 December 2003 13:10
To: amber_at_scripps.edu
Subject: Re: AMBER: xleap-N/C terminus

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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