AMBER Archive (2009)

Subject: Re: [AMBER] loading RNA sequence in xleap

From: FyD (
Date: Thu Sep 17 2009 - 04:39:09 CDT

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 &

Tutorials are available @

See in particular:

regards, Francois

Quoting gunajyoti das <>:

> 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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