Dear Amber Users,
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.
So here's what I thought of doing:
Generate Gaussian input with antechamber:
/> antechamber -i L02.mol2 -fi mol2 -o L02.com -fo gcrt -gv 1 -ge L02.gesp/
run Gaussian16 with L02.com as input
/> antechamber -i L02.gesp -fi gesp -o L02_resp.mol2 -fo mol2 -c resp -eq
/In L02_resp.mol2 Change the atom type of the anionic oxygen to OP
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.
How should I proceed and does it make sense to adapt the parameters in
the first place? Or are they possibly included in gaff2?
I would very much appreciate your advice!
Kind regards,
Andreas
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Thu Jun 29 2017 - 06:00:03 PDT
