Hi Vanessa,
I had a similar problem a while ago (Brian actually redirected you to a thread started by me with a similar problem). If I'm not wrong the way we got around it was by using the right topology files - after fiddling quite a bit I found Acpype did the best job and I did use .tbl files in the end. From what I recall I used the assignments for the small molecule from the 2D-NOESY in a .tbl file format and it managed to assign the 3D spectra based on that information. I'm sorry this is not more detailed but if the problem persists I can go over my notes and give you a more helpful reply.
Best wishes
Teresa Almeida
NMR spectroscopist, Analytical and Biological Sciences (ABS)
NIBSC - Blanche Lane, South Mimms, Potters Bar EN6 3QG
+44 (0)1707 641 202
-----Original Message-----
From: CcpNmr software mailing list <[log in to unmask]> On Behalf Of Vanessa Granitzka
Sent: 21 May 2019 14:22
To: [log in to unmask]
Subject: Aria2 cannot assign ligand peaks
Hi!
As I finished all preparations (topology, parameters, 3-letter code
etc.) to finally run some protein ligand calculations I've noticed that even though the ligand is present, the intermolecular NOEs are not.
At the very beinning aria2 masssages that some peaks of both spectra could not be assigned. Those appear to be the intermolecular ligand NOEs which I did assign on ccpnmr 2.4.2, but now are found in the peak_list.unassigned data. As a result, the ligand is floating around and never contacts my protein.
Does anyone have an idea at which point aria2 does not understand ccpnmr
2.4.2 assignments?
Best wishes,
Vanessa
--
Vanessa Granitzka, M.Sc.
Biomolecular NMR-Spectroscopy
NC 5/173
Faculty of Chemistry and Biochemistry
Ruhr-University Bochum
Universitaetsstr. 150
D-44801 Bochum
Tel.: +49 234 32-26246
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