On Thu, Oct 31, 2024, Maciej Spiegel wrote:
>
>Therefore, I can optimize the structure at PBE0-D4/def2-TZVP (+SMD solvent)
>and then use this optimized structure to derive charges with HF/6-31G(d),
>correct?
Yes.
>
>Regarding missing parameters in AMBER, is it acceptable to, for example, run:
>parmchk2 -i FDY.mol2 -f mol2 -o FDY_missing.frcmod -s parm10
>parmchk2 -i FDY.mol2 -f mol2 -o gaff2.frcmod -s gaff2
>and replace the “ATTN, needs revision” entries in FDY_missing.frcmod with the corresponding entries from gaff2.frcmod?
I think you need to run antechamber/parmchk2 twice, once using Amber atom
types and "-s parm10" in parmchk2, and a second time with GAFF atom types.
That is, in the first line above, you would need "-i FDY.amber.mol2" and in
the second line "-i FDY.gaff.mol2". But don't be afraid to experiment.
...good luck...dac
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Received on Sat Nov 02 2024 - 09:30:02 PDT
