[AMBER] Would AMBER suit my purpose?

From: Mignolet, Alex via AMBER <amber.ambermd.org>
Date: Thu, 30 Nov 2023 21:51:23 +0000

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 (ýB97M-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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Received on Thu Nov 30 2023 - 14:00:03 PST
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