I am studying a lipid transporting protein which can form a stable complex with lipid molecule. I have recorded all NMR data on the complex, detected intermolecular NOEs directly, etc. Now the question is - which software to use? I usually perform calculations in CYANA, but I don't know how to incorporate the lipid into the calculation. Maybe someone has the cyana library with the lipid molecules so I could have a look? Some instructions on how to calculate the complex structure in other software would also be very helpful.
Thanks in advance!
Hi!
Once I had a little peptide with a tert-butyloxycarbonyl (boc) and wanted to feed cyana with that staff. CYANA library is unfavorable regarding non amino acids because you have to deal with dummys in the library. Furthermore the calculation of the torsion dynamic was exhausting for CYANA which could be observed in the log file turning and turning around this boc :) CYANA is great but lacks a force field like CHARMM regarding such matters. An alternative is ARIA/CNS: Here you can incorporate the lipid with a topology and parameter cns-file or you define a new residue (lipid) in xml format for ARIA (http://aria.pasteur.fr/documentation/use-aria/version-2.2/non-standard-atom-or-residue-definitions). To make cns files acpype is quite good (http://code.google.com/p/acpype/).
Regards
Florian
Thanks, will try CNS. Didn't want to migrate, but seems that I have to :(
If you don't want to migrate from Cyana, I would recommend to ask Peter Guentert directly for the best possible solution. I like Cyana, but I would move to CNS in such case.
Best,
Innokentiy
You can do this without too much trouble in ARIA/CNS so long as you are prepared to generate topology & parameter file entries required for the small molecule (or can get hold of existing entries).
I drive my ARIA calculations from CCPN projects and have posted some info on how to get started with that here:
https://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/howtos-1/add-a-small-molecule
I have followed a similar path with ARIA to the web page you cite, but you also need to make some modification to the residue linking macros to keep your ligand separate.
Finally done it with CYANA, if anyone needs, can send the library for linker and LPPG, works quite ok.
Hi Konstantin!
Could you please share it with me?
I am using CYANA as well and would like to keep working in this program.
Olena
Hi Konstantin.,
Could you please help me. My aim is to solve also the structure of a peptide 4KDa into ND. I know this for some how a bigger complex between oligomers of the peptide an the ND PC/PG. I have problem even to get signal on the HNCA even if I deuterate the protein and I also try TROSY. What can i do to get information about CA and CB position?. I can easily transport the assignment of the monomer to the complex. But now I am looking for structure information. My concentration is limitaded also to max 50 uM.
Dear Konstantin,
I would like to know how you did the structure calculation for the complex with lipids. Thanks a lot.
Best,
-Xu
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