On Thu, Jun 29, 2017, Andreas Tosstorff wrote:
>
> I want to run a simulation with a Phosphorylated small molecule. The
> compound contains two monoanionic methyl phosphate groups. I came across
> the paper by Steinbrecher on Parameters for small organic compounds and
> wonder if it makes sense to adapt the parameters accordingly.
>
> Write an frcmod file with the optimal radius for OP as stated in the
> paper: 1.7493
> Or alternatively: load the frcmod.phosaa10
>
> I am a bit unsure about the last step. Because as far as I know, either
> way the parameters for interactions between gaff2 atom types and OP will
> be missing.
Correct: you will need to manually create a frcmod file that has this info,
basically copying the closest gaff bond and angle parameters, and change
the gaff oxygen type to OP.
The alternative, if your small molecule has atom types that are mostly
already in parm10.dat, is to ask antechamber to use Amber atom types rather
than the default gaff types. Either approach is likely to involve some
hand-tweaking.
...good luck...dac
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Received on Fri Jun 30 2017 - 11:30:04 PDT
