Dear Wu,
> I want to do MD simulation of 137 nt RNA by keeping phosphate groups
> neutral. I found from Amber Archive that RAN, RCN, RUN and RGN will keep
> the nucleotides of RNA neutral
If you want to generate a new RNA fragment, you could use the R.E.D.
III.4 tools or R.E.D. Server 2.0. See
http://q4md-forcefieldtools.org
A _nucleotide_ fragment for a nucleic acid (NA) is generally built
using two molecules:
dimethylphosphate + the modified _nucleoside(s)_
See
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
If you use R.E.D. Server, a Java applet is generated in the graphical
interface to display the FF library generated (at the end of the job;
i.e. a mol2 file).
R.E.DD.B. contains already neutral NA: look for the following author:
Lei Tao (Texas A&M University).
Concerning geometry optimization of RNA nucleosides, you might be
interested by avoiding canonical hydrogen bonds between the HO2 & HO3
hydroxyls. If you search once again in R.E.DD.B. by using the keyword
'RNA' you will get several project codes.
In your case you need to create a new force field topology database
(FFTopDB) for neutral RNA. If you use R.E.D. Server; you first create
5 P2N files, you add definitions for charge constraints in these 5
files, and you finally run R.E.D. IV: You will get all what you need
(the neutral RNA FFTopDB) in a SINGLE R.E.D. IV job.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
I hope this helps.
regards, Francois
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Received on Wed May 18 2011 - 02:00:03 PDT
