Hi James,

We've been dealing with the same issues in Glasgow and have a near complete solution (as evidenced by finished structure calculations) . I'm off campus for the rest of the week but if you can be patient I will post the recipe soon.

Brian

--
Dr Brian O Smith
MCSB, MVLS, University of Glasgow

---- James Garnett wrote ----

Dear all,

We have recently used CCPNv2.4 to assign a 19-residue peptide with N-terminal acetylation and C-terminal amidation. The capping has been defined as residues ACY and NH3 in CCPN. Does anyone have any experience carrying out Ac/NH2 capped peptide structure calculations in ARIAv2.3 with projects imported from CCPN. We are having issues with ARIA not recognizing the ACY/NH3 residues and attempts to modify topology/parameter files in aria/cns etc have failed so far. After extensive googling the only related problems I can find are from over five years ago and are not straightforward fixes. I figure that this should be a standard procedure by now so I am hoping that someone can pass on a standard fix to using ARIA/CCPN and if not can suggest an alternative approach.

Many thanks in advance

James

Dr James Garnett
Lecturer in Structural Biology
Queen Mary University of London
Department of Chemistry & Biochemistry
School of Biological and Chemical Sciences
Room G.04, Joseph Priestley Building
Mile End Road
London E1 4NS
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Tel: +44(0)20 7882 8446
http://www.sbcs.qmul.ac.uk/staff/jamesgarnett.html
https://garnettlab.wordpress.com



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