Dear Amber community,
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?
I would appreciate it if could guide me on setting-up such a system.
regards,
jenk
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Received on Sun May 11 2008 - 06:07:58 PDT
