Re: [AMBER] "An All-Atom Force Field for Metallocenes"

From: Gustaf Olsson <>
Date: Tue, 10 Aug 2021 12:13:06 +0000

As usual, turns out that adopting parameters were not as straight forwards as initially hoped.

Charges and types seems pretty easy to transfer to a mol2 file. Mass, well that fits nicely in an frcmod file. The epsilon values are, if I understand this correctly, transferable between “OPLS-AA” based parameters and Amber though I do not see exactly how this could be defined in an FRCMOD file. It also turns out that what I was looking at was previously discussed DL-Poly parameters “easily adaptable to opls”.

Sigma need to be recalculated/adjusted and parts of the dihedral information seems to need recalculation/adjustment. There is a section with, what I’m guessing are "Fourier coefficients for dihedral angles”, that would need to be processes in some manner as well.

The actual text on the amber file format site literally states "Of course, major changes, such as using the AMBER/OPLS force field rather than the AMBER one, would best be made by changing this file” so I suppose the mol2/frcmod route is not as reasonable as initially thought. I suspect there is additional unit conversion needed for bonds, angles and dihedrals as well as the "V1 V2 V3" section, which as a best guess could be "Fourier coefficients for dihedral angles”.

I’m starting to suspect that “easy adoption” of these parameters is a much larger project then I will be able to finish with the allocated amount of time for the entire project.

Any suggestions and feedback is welcome and much appreciated

Best regards
// Gustaf

> On 10 Aug 2021, at 10:28, Gustaf Olsson <> wrote:
> Hello Amber forums
> While trying to figure out if could be a possible solution for a ferrocene monomer I am working with I was looking at a set of published parameters "An All-Atom Force Field for Metallocenes” by Lopes, Couto and Piedade (10.21/jp0628961).
> Has anyone adapted these parameters for simulations using the Amber simulation package? I assume that these parameters could be adapted using a mol2 and frcmod file?
> I am a bit confused by the “dummy cp centroid” used, possibly based on the terminology used. I assume there is a center of mass “dummy atom” defined (Xcp) though I am still a bit unsure regarding this assumption.
> If anyone has any experience regarding the use of these parameters, or any other parameters for simulation of ferrocene terminated strictures with AMBER, I would really appreciate any feedback and/or material.
> Likewise, if there are any reflections regarding the idea of trying to adopt these parameters using mol2 and frcmod files (suggestions on different approaches or just general advice), this would also be greatly appreciated.
> Best regards
> // Gustaf

AMBER mailing list
Received on Tue Aug 10 2021 - 05:30:02 PDT
Custom Search