Hi Alex,
just my two cents on what is a very broad question on which others may have
other opinions. Amber can do something like what you describe, but getting
a mixed solvent simulation with some random organic molecules to run
properly and validate that it creates a useful condensed phase system is
easily something you can spend your entire masters project on getting right.
Also: fixing bond, angle and dihedrals is possible in Amber but it does not
make your calculations more efficient, usually non-bonded interactions make
up the bulk of the computation, the bonded terms are almost irrelevant.
Second, MMFF is one force field out of many, not very commonly used in
Amber and (better?) alternatives are available.
Maybe have a close look at the tutorials on the Amber homepage to see what
is possible, but with mixed solvent simulations you are picking a somewhat
rare advanced application right at the start.
Kind Regards,
Thomas
On Thu, Nov 30, 2023 at 10:51 PM Mignolet, Alex via AMBER <amber.ambermd.org>
wrote:
> **Warning** The sender address ("Mignolet, Alex via AMBER" ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> Hello, my name is Alex Mignolet. I am a master's student at California
> State University Sacramento, and I am learning computational chemistry. As
> such, I am new to computational programs, especially prompt based ones such
> as AMBER and ORCA. As such, I appreciate any help you can provide.
>
> I am working on a project where I need to use mixed solvation models with
> small organic molecules. I am concerned that the location of the solvent
> molecules is not optimal, and as such, would like to use AMBER to optimize
> them. To check many orientations, I would like to use MMFF, Monte-Carlo,
> and lock the bond distances, bond angles, and bond dihedral angles in both
> the solvent and solute so that only their location and orientation may be
> changed. In my mind, this would make the computations extremely efficient
> and would allow for a fine search of phase space in a short period of time.
> I was drawn to AMBER as the manual states that it allows for restraints on
> molecules as well as modifying the weights of terms in the MMFF
> optimization, which would enable the type of calculation I had in mind. It
> also states that additional intermolecular parameters can be added, such as
> a polarization term, which would be extremely beneficial in my case.
>
> I would then use DFT (B3LYP/6-31G*) in Spartan (Student Version) to
> finalize the structural optimization and then run the thermodynamic
> calculations in ORCA (ωB97M-V/def2-QZVPP).
>
> My questions are as follows. Is what I envision using AMBER for feasible?
> Additionally, as I am very new to prompt based computational softwares,
> could you please provide an example prompt/set of options that would
> achieve the desired results?
>
> Thank you,
>
> Alex Mignolet
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--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
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Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Fri Dec 01 2023 - 00:30:02 PST
