On Sun, May 04, 2014, sammia khatak wrote:
> HelloI have prepared .prmtop, .inpcrd and pdb files of protein ligand
> complex in water. Now i want to run energy minimization. i just want to
> know whether i should do it with sander or namd and if sander is used
> can i further continue it on namd. how far are these two compatible. And
> is there easy way to generate PSF of this complex from pdb to run in
> namd.
There is a link at
http://ambermd.org on "using the Amber force field in
namd", which walks you through the details of this.
That said, it is a multi-step process, and you have to be rather careful.
Unless you have a good reason to want/need to use namd, I'd recommend
continuing with either sander or pmemd.
...dac
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Received on Sun May 04 2014 - 09:00:02 PDT
