AMBER Archive (2008)

Subject: Re: AMBER: parmbsc0 parameters for RNA.DNA systems

From: David A. Case (case_at_scripps.edu)
Date: Sat May 10 2008 - 10:27:36 CDT

On Sat, May 10, 2008, Cenk (Jenk) Andac wrote:
>
> I would like to set up prmtop and coordinate files using the parmbsc0
> parameters in LeaP for a biomolecular system in which a 5-nt ssRNA base pair
> with a 5-nt ssDNA.
> Is it allright if I use leaprc.ff99+parmbsc0 parameters for the ssDNA and
> leaprc.rna.ff99+parmbsc0 parameters for the ssRNA and then combine each
> strands to make a double stranded RNA.DNA system in one Leap job?

You can set up mixed RNA/DNA systems pretty easily. Just use the full Amber
residue names (like DA or RA) in your input pdb file, rather than ambiguous
alternatives like "A" or "ADE".

...good luck....dac

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