AMBER Archive (2006)

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

From: anna ferrari (ferranna_at_unimo.it)
Date: Wed Jun 28 2006 - 11:43:41 CDT

Hi Ray

> 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.

I haven't used identical parameters for SASA calc. For MMGBSA I set
surften=0.0072 and surfoff=0.00 as was in the default input file and for
MMPBSA surften=0.00542 and surfoff=0.92 that should be for parse radii.
With radiopt=0 and proc=2 in MMPBSA calc, what SASA parameters are correct?
Thank you again
Anna

> 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
>>

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