On Sun, Nov 12, 2023, He, Amy via AMBER wrote:
>
>
>I have a question about the main parameter sets in Amber, specifically,
>gaff2.dat and parm10.dat. I was checking these files and trying to get
>a sense of the force constant of an improper dihedral, for example, the
>improper torsion in a carboxylate group C(=O)O.
>
>
>In gaff2.dat, the improper section begins with:
>X -o -c -o 1.1 180. 2. JCC,7,(1986),230
>X -X -c -o 10.5 180. 2. JCC,7,(1986),230
>
>However, in parm10.dat I saw…
>X -X -C -O 10.5 180. 2. JCC,7,(1986),230
>X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230
>
The intent is that specific dihderals alway overwrite more general ones
(i.e. ones with wild-cards.) In the second case above, it doesn't make any
difference, since the two potentials are the same.
In GAFF, if you are concerned about what value you are getting, use parmed
to interrogate your prmtop file, to find out for sure that you are getting
what you want.
>Ps. On the referenced paper (https://doi.org/10.1002/jcc.540070216),
>both got a force constant = 10.5. But I understand if it was modified
>for particular reason like to balance with the other GAFF parameters. I
>was just curious if I need to reuse the GAFF parameters for validation
>purposes, which should I choose? 1.1 or 10.5?
This question is beyond my level of knowledge.
...good luck...dac
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Received on Mon Nov 13 2023 - 09:00:03 PST
