AMBER Archive (2009)
Subject: Re: [AMBER] loading RNA sequence in xleap
From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 17 2009 - 04:39:09 CDT
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/ &
Tutorials are available @ http://q4md-forcefieldtools.org/Tutorial/
See in particular:
Quoting gunajyoti das <guna_das78_at_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.
> Neh university
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