On Fri, Jun 01, 2018, Jing Wang wrote:
>
> I am thinking to get the AMBER Certified Workstation currently put forth
> by Exxact Corp, because the speed is very impressive to compare with
> the Schrodinger Desmond that I am currently using. However, I remember
> that in my old days the force-field parameters for small molecule
> compounds needed to be developed each time to run AMBER or CHARMm. I
> wonder what is the situation now. Can I get the program that generates
> or help the user to generate these parameters? The situation with
> Desmond/Schrodinger suite is that the GUI automatically generates or
> assigns OPLS3 force-field to any compounds and at the user's choice, a
> Force-Field Builder module can generate torsional angle profiles to new
> chemotypes effortlessly. Can you tell me what is the situation for AMBER
> and whether or not the whole process is available for an industrial
> user?
>
> I talked with Exxact Corp people and they said that I have to ask
> you this question. They do not know if the code pre-installed on the
> machines is good enough. I would greatly appreciate if you can answer my
> question and help me make a decision.
Amber has a very automated procedure, built on the generalized Amber
force field (GAFF2) procedure. The basics are described in this
tutorial:
http://ambermd.org/tutorials/basic/tutorial4b/index.html
It is straightforward to script this procedure into a virtual screening
(or other) workflow. Everything you need is available in AmberTools,
and doesn't require any specialized hardware. (That is, you can check
out how things work without needing anything more than a laptop
computer.) We also have tools for optimizing individual torsion
potentials (as opposed to taking the GAFF predictions), but these are
less well automated.
GAFF has been very widely used for more than a decade, so you can find
lots of examples of its strengths and weaknesses; and of course, make
your own tests. I am personally not "up" on comparisons between OPLS3
and GAFF, but maybe others on the list can chime in.
(If you have access to the OPLS3 parameterization, you could also
consider converting those to Amber format.)
....dac
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Received on Sun Jun 03 2018 - 09:30:03 PDT
