Thanks, Rasmus, the name should have been sort of obvious, but I managed somehow not finding it... I probably have to attach the link to make use of it in ARIA.
Krisztina
--- On Fri, 10/19/12, Rasmus Fogh <[log in to unmask]> wrote:
From: Rasmus Fogh <[log in to unmask]>
Subject: Re: adding C terminal amide cap to a peptide
To: [log in to unmask]
Date: Friday, October 19, 2012, 5:37 PM
Dear Krisztina,
Good news and bad news:
The good news are that we have one, it is called molType 'other', ccpCode 'Nh2', and you cn find it in the molecule:Molecules {Small Compounds} tab
The bad news it that (like most non-standard ChemComps) it has not got any of the links and hooks that allow you to connect it up to other residues. Still, or practicla purposes it should be OK. Add it as a last residue, and set the C-termnial residue to linking 'middle'. You will have the atoms you need, to assign to, even if the program does not know that there is a bond between the CO and the NH2. For exactly how to do it, see the Wiki.
Alternatively, you can use ChemBuild to make wither a properly linked NH2, or a capped residue.
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Fri, 19 Oct 2012, Krisztina Feher wrote:
> Dear All,
>
> I am looking for a ChemComp to make a C terminal amide group capping, but I do not find it. I am guessing that such a cap should already exist and I do nto have to make a ChemComp for it. Any insight is most welcome. Thanks!
>
> Krisztina
>
