> I have protein-rna complex. I opened xleap as follows
>
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> Then i opened my pdb with loadpdb command. What i would like to know is
> that
> in this case, will xleap automatically assign ff99 params to rna and ff99SB
> to the protein. Or pricesely is this the correct way to use ff99SB + ff99
> combination for protein and RNA.
If your pdb residue and atom names agree with the templates,
all should happen automatically on loadpdb. If not you will see
messages about unknown residues or atoms on loadpdb, and you will
get more error messages with saveamberparm.
Bill
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Received on Wed Aug 11 2010 - 10:30:02 PDT
