AMBER Archive (2006)

Subject: AMBER: MM-PBSA and gaff atom types

From: anna ferrari (ferranna_at_unimo.it)
Date: Tue Jun 27 2006 - 04:28:03 CDT


I would like to calculate binding energies of ligands inside a protein using
MM-PBSA and MM-GBSA with AMBER 8. In the topology of the complex, the
ligands
are described with gaff atom types, the protein with AMBER atom types
(mixed).
For PB, we are using PBSA of amber 8 with RADIOPT=0 (i.e. radii read from
prmtop file). For GB, igb=5 and gbsa=1 are used. For both PB and GB,
mbondi2 radii
have been set in the topology file. We found that PBTOT and GBTOT
binding energies of different ligands calculated on exactly the same
structure
of the complex do not correlate. Is it possible to use PBSA with gaff atom
types?
Also, the net charge of the protein is 15. Would it be better to
neutralize the
protein before MM-PBSA calc?
Thank you for your help

Anna

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