Re: [AMBER] loading RNA sequence in xleap

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 17 Sep 2009 11:39:09 +0200

Dear Gunajyoti,

You need to develop a new FF library for inosine fragment(s).
You could use R.E.D. or R.E.D. Server for that.

See http://q4md-forcefieldtools.org/RED/ &
     http://q4md-forcefieldtools.org/REDS/

Tutorials are available . http://q4md-forcefieldtools.org/Tutorial/

See in particular:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#18
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25

regards, Francois


Quoting gunajyoti das <guna_das78.yahoo.co.in>:

> hello amber users,
>           I tried to load a double stranded tRNA sequence having a
> minor RNA base INOSINE ( the sequence had been taken from pdb 1XNQ)
> in xleap. I used leaprc.rna.ff02 force field to start xleap, but
> unfortunately xleap could not recognise the INOSINE residue. I even
> loaded the all_modrna.ff08.lib, hoping that the situation will
> improve, INOSINE still remained unrecognised by xleap.
>          
>           When I tried loading another double stranded RNA sequence
> having all standard residues ( G and C), I could easily generate the
> prmtop and inpcrd files.  
>   
>           Am I choosing a wrong force field for the INOSINE
> containing sequence?
>   
>           Kindly help me out.
>      
>           with regards, thanking in advance.
>  
>     Gunajyoti
>     Neh university  



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Received on Thu Sep 17 2009 - 03:00:02 PDT
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