AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA and gaff atom types

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Jun 27 2006 - 21:47:51 CDT

Anna,

If you set radiopt=0, pbsa should use the radii in the prmtop files, and
this is independent of what atom types are used. To confirm this, you
can set pbverb=1 in pbsa.in (input file for pbsa). The radii will be
printed in the pbsa output file.

As for the poor correlation between PB and GB binding free energies,
have you used identical SASA parameters? I think the default SASA values
are different for MMPBSA and MMGBSA in AMBER 8.

All the best,
Ray

anna ferrari wrote:

> 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
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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