AMBER Archive (2008)

Subject: Re: AMBER: LEap error message for parmBSC0 force field

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue Apr 01 2008 - 18:55:38 CDT

> I keep getting the following error message
> when I try to save a topology file for a 2nt RNA molecule
> using the new parmBSC0 force field. Could someone please
> clarify if I am missing something with the installation of the
> parmBSC0 force field?
>
> >verbosity 2
> > x=sequence {RA5 RG3}
> Sequence: RA5
> Sequence: RG3
> Joining RA5 - RG3
> > edit x
> > saveamberparm x a.prmtop a.x

...without seeing what you are loading (in terms of the leaprc and what
residue/topology, library, or parameter files) it is tricky to determine,
but my guess is that you didn't load-up all the necessary library/force
field files as it is complaining about impropers...

I would try:

tleap -f $AMBERHOME/dat/leap/cmd/leaprc.rna.ff99
bsc0 = loadamberparams frcmod.parmbsc0

followed by the rest of your script.

-- tec3
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