Re: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation

From: german <gsciaini.qi.fcen.uba.ar>
Date: Thu, 16 Feb 2006 09:04:39 -0300

Dear zgleo,
A value of -134 Kcal/mol is aprox. the interaction between ions...(with +1
and -1 charges), continuum solvent models are useful for describing
long-range interaction effects but fail when describe first solvation shell
effects. You should consider to add explicit solvent molecules (plus a
continuum model if you wish). Another problem is to consider to add
contra-ions to compensate the -2 charge...

good luck...

GS.




At 02:04 p.m. 16/02/2006 +0800, you wrote:

>Dear amber users
> I want to calculate the binding free energy of a protein (222 AA)
> with a 7-AA peptide, in which a phosphorylated Thr (pThr) is included.
> The pThr is -2 charged according to the parameters contributed by Sticht
> et al. (http://pharmacy.man.ac.uk/amber/). However, the value of PBTOT
> given by MM_PBSA method is very large (-134.65 kcal/mol). I guess that
> the electrostatic energy between pThr and the protein may be estimated
> too much under contium solvent model. Any suggestion is welcome!
>
>
>
># COMPLEX RECEPTOR LIGAND
># ----------------------- -----------------------
>-----------------------
># MEAN STD MEAN STD MEAN
> STD
># ======================= =======================
>=======================
>ELE -7721.30 42.67 -7209.03 43.95 -177.59
> 8.02
>VDW -980.30 20.38 -927.82 20.13 1.01
> 2.98
>INT 4786.40 46.57 4625.89 47.10 160.51
> 7.55
>GAS -3915.20 48.01 -3510.96 51.07 -16.07
> 11.34
>PBSUR 60.11 0.81 60.30 0.79 5.91
> 0.07
>PBCAL -3876.45 31.21 -3789.96 32.87 -346.11
> 6.82
>PBSOL -3816.33 31.03 -3729.66 32.89 -340.20
> 6.83
>PBELE -11597.75 28.53 -10998.99 21.75 -523.69
> 4.87
>PBTOT -7731.54 36.46 -7240.62 40.49 -356.26
> 9.14
>
># DELTA
># -----------------------
># MEAN STD
># =======================
>ELE -334.69 16.98
>VDW -53.49 4.50
>INT 0.00 0.00
>GAS -388.18 15.86
>PBSUR -6.09 0.08
>PBCAL 259.62 15.61
>PBSOL 253.53 15.61
>PBELE -75.07 11.08
>PBTOT -134.65 8.52
>
>
>Best regard!
>
>        zgleo
>          2006-02-16
>___________________________________________
>
>Zhiguo Liu
>Ph.D candidate
>Drug Discovery and Design Center
>Shanghai Institute of Materia Medica
>Chinese Academy of Science
>Shanghai, China
>zhiguo.leo.gmail.com
>zgliu.sibs.ac.cn
>___________________________________________
>
>
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