Hello! I trying to do some molecular dynamics with DNA structures, where I am checking how 5' phosphate affects the interaction. However, in common force field such as AMBER, no charge set was defined for the phosphate. Does anyone know any other force field can do the job, or how could I add proper parameters for 5' phosphate in current force field like AMBER99bcs1?
Zhe Li I am not pretty sure but I guess latest charmm force field should make it parametric.
Thanks, Dr Thirumal Kumar D . I just gave a try of CHARMM36, but it automatically deletes the 5' phosphate when doing model building.
Martin Klvana , any more information on the DNA_CI.lib? Is it some file where I can change parameters?
Not sure whether I did every step properly. I also attached a simple model here, which I plan to minimize energy, without deleting the phosphates at 5' ends.
Zhe Li, yes, dat/leap/lib/DNA_CI.lib is a text file, included in AmberTools:
http://ambermd.org/GetAmber.php#ambertools
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