On Sat, Sep 18, 2010 at 07:49, case <case.biomaps.rutgers.edu> wrote:
> It's a little tricky, since Amber has the SPC/E water model "built-in", but
> not SPC itself. You would have to create an SPC parameter file (just by
> analogy to the one for SPC/E), then load that plus you PDB file into LEaP, and
> issue a "saveamberparm" command.
SPC/E is perfectly fine actually. I'm actually just looking for the
set of commands in leap, because everything I've found requires a box
to already exist with some solute, etc. I realize this is probably
very simple but I have little experience with Amber and I haven't
found a direct approach. Once I understand how to actually get it to
function I can do anything I need to do by modifying parameter files.
Best, Anthony
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Received on Sat Sep 18 2010 - 10:00:03 PDT
