On Tue, Jul 20, 2021, Maximilian Ebert wrote:
>I have my own prmtop write to create an input forcefield to pmemd. I
>could find all the necessary information to parameterize the protein /
>ligand from the forcefield files provided in the dat folder of the amber
>installation. The only section I can’t write is the RADII and SCREEN
>section to fully support all GB modes. I would like to know where tleap
>looks to write this section. Where do these numbers come from? Which
>parameter files are read to fill the section with the appropriate values
>for the corresponding atom types. We cannot depend on the amber tools and
>hence are trying to write a fully compliant prmtop file.
Look in amber20_src/AmberTools/src/parmed/parmed/tools/changeraii.py.
That has python code for assigning radii and screening parameters. You
should be able to adapt this to your codes.
....good luck...dac
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Received on Tue Jul 20 2021 - 08:30:02 PDT
