AMBER Archive (2005)

Subject: Re: AMBER: capping

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Apr 28 2005 - 11:21:03 CDT

Quoting amit_at_mbu.iisc.ernet.in:

> I have drawn those missing hydrogen atoms at the N terminal of free
> methionyl molecule but how to assign charge to the newly added hydrogen
> atoms. Since none of the options on the menu bar are able to assign
> charge.

If you have a new residue that you have 'capped' with ACE & NME, this means you
need to build a new PDB file for ACE-XXX-NME. But then you need to calculate the
RESP charges for this new UNIT 'XXX'.
This has been already several times discussed:
See in particular:
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#27

Regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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