Re: [AMBER] md simulation of modified nucleotides in RNA

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 17 Apr 2018 06:30:41 +0200

Dear Leila,

> Can I use Amber for md simulation of modified nucleotides in RNA?

You might try PyRED at RED Server Dev.
http://q4md-forcefieldtools.org/REDServer-Development/

See tutorials:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
   and in particular how to generate molecular fragments from whole
molecule(s):
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#2
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#19
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#27

In your case you likely have to start from modified RNA
nucleo_s_ide(s) + dimethylphosphate whole molecules to create modified
nucleo_t_ide fragments.

regards, Francois


           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/


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Received on Mon Apr 16 2018 - 22:00:02 PDT