Re: [AMBER] Forcefield for Modified RNA

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 03 May 2011 11:20:10 +0200

Dear Hari Krishna,

> I need to do the simulation of the modified oligonucleotides in mRNA. The
> modification is 2'-methoxy 4'-aminomethyl uridine, what is the force field I
> can use for the simulation. Is there is any force field for this specific
> modification. And also what are the things necessary to take care while
> doing the modified RNA simulation

If no FF library is available, you could use R.E.D. III.4 or R.E.D.
Server 2.0 .
http://q4md-forcefieldtools.org/

Tutorials are available .
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25

regards, Francois



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Received on Tue May 03 2011 - 02:30:05 PDT