I have a system of DNA and a certain molecule that shows good docking energy with DNA. I want to run the simulation in gromacs. The parameters I should use for DNA is amberff99parmbsc so I tried getting parameters for the molecule as per the tutorial using parmcheck and acpype. Unfortunately one of the elements of my molecule is non-standard element so the tutorial doesn't seem to work. My question is do we have some other way to get the forcefield parameters for the new molecule? My second question is can I use CHARMM parameters for my molecule and AMBER for DNA?
if you use moltemplate ,update its Oplsaa reference by adding all the characterization for your element and it should generate your forcefield.
second question ,yes but when you do your simulation consider both parameter as if the molecules was separated systems.
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