AMBER Archive (2008)

Subject: AMBER: parmbsc0 parameters for RNA.DNA systems

From: Cenk \(Jenk\) Andac (
Date: Sat May 10 2008 - 08:47:50 CDT

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.



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