I'll definitely read around your suggestions. Initially I thought to use different angle parameters for the same ag-cc-na angles since some of the chemical environments differ slightly but I suppose the point of gaff assigning them to be the same three atom types is that it thinks they're the same/degenerate? I say this because I remember my PhD supervisor saying he assumed I'd eventually have one angle parameter value which may or may not just be averages of the four I have, which I'm guessing ties in with them all being the same atom types. The other issue is that not all of my angles are the same value (some can vary up to around 10 degrees) so I don't know if that would necessitate using different angle parameters for different angles since you specify an angle value in frcmod files (I think?)
I'll read around your suggestions
Thank you
Sam
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________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, December 22, 2021 8:19:28 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue with defining angle parameters in frcmod files
I don't know of any easy way to do that. The purpose of atom types is to
control which parameters are applied. If you want different parameters,
then you should probably use different atom types. Once the prmtop is
built, the angles are listed separately for each set of 3 atoms, but each
just has a pointer into the angle parameter list where the force constant
is stored. In principle you could change that pointer, but the alternate
parameters would need to already be in the prmtop, and they won't have been
added unless they matched something else in your system. There are ways to
edit more extensively (manually adding parameters to the angle parameter
list in the prmtop, but not trivial if you aren't very familiar with the
format (see
https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Fprmtop.pdf&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cf578bd42ed8f4fb46c8f08d9c5889980%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637758013076246668%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mxCFa2wt0mpm703OvSWrRT5fGiE94a1XE6ffeDFS71Y%3D&reserved=0).
I think that the best approach would be to use different atom types for the
atoms that differ between these ag-cc-na angles. You can duplicate the
existing parameters for the new atom type using the existing ones in your
frcmod, then edit the ones that you want to change. In my experience that's
much easier to edit at the frcmod level than at the prmtop level (and would
be re-usable if you do something similar in the future, rather than always
having to edit the prmtop).
there might be a way to do this with parmed, but I'm not aware of it. There
also may be other tools for doing this kind of editing - maybe other on the
list will have better suggestions.
On Wed, Dec 22, 2021 at 2:22 PM Sam Walsworth (Researcher) <
Sam.Walsworth.hud.ac.uk> wrote:
> Hello,
>
> I have a molecule that has four angles made up of the same three atom
> types in a row (ag-cc-na) whereby each of the four angles has its own
> unique angle parameter (in kcal/rad^2). I'm assuming that if I defined one
> of the angles in the frcmod file, it'd automatically apply that parameter
> and angle value to all four ag-cc-na angles since they're made of the same
> atom types.
>
> Is there a way I can specify which atom name and/or atom number I want the
> angle parameters applied to such that I can parameterise the different
> angles appropriately?
>
> Sam
> University of Huddersfield inspiring global professionals.
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