AMBER Archive (2009)

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

From: case (
Date: Thu Sep 17 2009 - 07:13:38 CDT

On Thu, Sep 17, 2009, gunajyoti das wrote:

> 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.

This probably means that the residue name used for inosine in your pdb file
doesn't match the residue name for inosine in the all_modrna.ff08.lib file.

After you load the modrna library, you can use the "list" command in LEaP to
see what residues it knows about, then make sure your PDB file uses the same
residue and atom names as the library.

Finally, be sure that you really want ff02, rather than the more widely tested
ff99 or ff99bsc0 force fields. I doubt that the modrna modified bases are
compatible with ff02 (you should check).

...good luck...dac

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