[AMBER] RNA with Malachite Green simulation

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Tue, 7 Oct 2014 20:15:31 +0000

Dear Amber Users,

I would like to explore the dynamics of an RNA Malchite Green (MGR) aptamer with the MGR
included. I am looking for the prep and frcmod files, if available. Is there a public source for them?
I did not find MGR in the AMBER parameter database (http://www.pharmacy.manchester.ac.uk/bryce/amber).
The closest I got to the answer was in the publication by Beierlein at al., ACS Langmuir, 29, 2013.
The bottom line is, do I need to do my own prep (partial charges from the above publication or Gaussian
plus Antechamber; please, correct me if I am missing something) or could someone point me in the right
direction or kindly share their prep and frcmod files. Perhaps the issue is more complicated than I think.
Atoms names are, of course, different in the PDB # 1Q8N (NMR RNA + MGR structure) and in the above
mentioned publication, but the structures are identical.

Any advice would be greatly appreciated.

Thank you in advance, Voytek Kasprzak

Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research, Frederick, MD.
(301) 846 5537

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Received on Tue Oct 07 2014 - 13:30:02 PDT
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