[AMBER] MMPBSA binding energy was positive for charged ligand

From: Nada Afiva <nadaafiva.gmail.com>
Date: Mon, 21 Sep 2020 09:24:56 +0700

Dear Amber:

I was preparing a system for ATP complexed with RNA and protein using
AM1-BCC charge, then performed 100 ns MD simulation and calculating the
MM-PBSA binding energy.

If I used the charge for ATP=0 in the preparation step, then the MMPBSA
final binding energy was around -30 kcal/mol, however when I used the
charge for ATP=-4, then MMPBSA final binding energy become positive.

All other parameter was the same in both systems.

Here is the input file:

Input file for running MMPBSA
| startframe=0, endframe=50000, keep_files=2, interval=250,
| verbose=2,
| igb=5, saltcon=0.100
| istrng=0.1, exdi=80, indi=4.0,
| inp=1, cavity_surften=0.0378, cavity_offset=-0.5692,
| fillratio=4, scale=2.0,
| linit=1000, prbrad=1.4, radiopt=0,

Please any suggestion why the difference was very contrast.

Thank you in advance.

Best regards,

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Received on Sun Sep 20 2020 - 19:30:02 PDT
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