On Tue, 2013-11-19 at 20:22 +0800, liu fengjiao wrote:
>
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>
>
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>
> ---------- Forwarded message ----------
> From: Jason Swails <jason.swails.gmail.com>
> Date: 2013/11/18
> Subject: Re: [AMBER] which PBRadii is best when we use PBSA method to
> calculate the bonding affinity
> To: AMBER Mailing List <amber.ambermd.org>
>
>
>
> On Mon, 2013-11-18 at 15:32 +0800, fjliu wrote:
> > Hello everyone !!
> > I am using MM-PBSA approach to calculate the binding free energy of
> a ligand with the protein,there is a great difference of the results
> when I changed the PBRadii from mbondi to mbondi2 in my leapin
> files,at the same time I kept other parameters as the same,so I want
> to know which PBRadii is the best for we calculate the bonding free
> energy.
> >
> > Please provide valuable suggestions in this direction and if
> possible relevant articles based on similar concept.
>
>
> This depends entirely on the solvation model you're using.
>
> As always, if you want specific answers you need to give more specific
> details about what it is you're doing. What model are you using?
> Which
> energy terms differ the most, and in what models? etc.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> I am using the MM-PBSA approach to calculate the binding free energy
> of biotin with wild type streptavidin(protein ID 1MK5),I solvated the
> complex with TIP3PBOX 12.0,and I used the PB model to calculate ,the
> mainly energy difference comes from PBCAL(the electrostatic
> contribution to the solvation free energy calculated by PB) and
> PBELE(sum of the electrostatic solvation free energy and MM
> electrostatic energy).I calculated the binding free energy with the
> leapin files as below :
>
> source /usr/local/amber12/dat/leap/cmd/oldff/leaprc.ff03
> source leaprc.gaff
> set default PBradii mbondi
> MOL=loadmol2 ../../../ligand_parameter/ligand_g03/ligand.mol2
> loadamberparams ../../../ligand_parameter/ligand_g03/ligand.frcmod
> pro=loadpdb protein_modloop2_a.pdb
> lig=loadpdb ligand_ac_a.pdb
> com = combine { pro lig }
> saveamberparm pro protein_gas_a.top protein_gas_a.crd
> saveamberparm lig ligand_gas_a.top ligand_gas_a.crd
> saveamberparm com complex_gas_a.top complex_gas_a.crd
> quit
>
>
> But when I change the PBradii mbondi to mbondi2 ,there is a great
> difference of the results.
Then I suppose the choice of radii is important. I don't know what the
'best' choice is. I also don't know what you mean by "great difference
in the results". It's likely that the difference is less than the
accuracy of the method itself.
Also, absolute binding free energies are typically very bad with MM/PBSA
analyses. It's the relative binding free energy that is more reliable.
The real test is whether you get different relative binding free
energies with the different radii sets.
> Also I have another question , I used the gmail box registe the amber
> mail list ,then I can't receive your reply for my question,but I can
> receive the email from others and I didn't prevent the email from
> anyone in my mailbox sets .I just know from my partner that you have
> already answered for me ,this question also happened on my other
> partners.
I don't know what happened here. Check your SPAM folder, maybe. I use
gmail with no problems.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 19 2013 - 05:30:04 PST
