Hi Dimitrios --

This is strange.  Can you send us the input files (and ideally the PDBs, if you're able) so we can take a closer look at this?

Thanks,

Nathan

On Apr 22, 2009, at 7:17 AM, Dimitrios Spiliotopoulos wrote:


Good morning!


I recently started using APBS, and I tried to perform the
polar solvation calculations in two different ways: in the first case, I write three different input files (one for each component: complex, protein and ligand), perform three distinct runs and calculate the difference (i.e., Gcomplex - Gprotein - Gligand) from those values; in the second case, I write one input file only which basically contains the three previous input files and prints out the aforementioned difference.
I'm writing you in order to ask you how come I obtain a strange results.
The variation obtained with the single input file (the latter case) is different from the variation calculated from the results of the
three distinct runs: indeed, the absolute value of the complex is the same in both cases. What changes are the values of the protein (around 10% of the absolute value) and the value of the small ligand, which is one order of magnitude lower if the calculation is performed in a distinct manner.
With that being said, the
variation obtained with the single input file it is inescapably the negative of the "Global net ELEC energy" calculated for the complex in the single-input-file case.

I would also like to ask you whether there is need (and if so, if there's a way) to combine the values
polar solvation calculations grid spacings and those of the apolar solvation calculation quadrature grid spacings.

Thank you very much in advance,

Dimitrios Spiliotopoulos

_________________________________________________________________________________________________

Dulbecco Telethon Institute c/o DIBIT Scientific Institute
Biomolecular NMR Laboratory, 1B4
Via Olgettina 58, 20132 Milano (Italy)
Tel     : 0039-0226434348/5622/3497/4922
Fax    : 0039-0226434153
Email : spiliotopoulos.dimitrios@hsr.it; dimitris3.16@gmail.com
Skype: dimitris3.16


_________________________________________________________________________________________________

THREE INPUT FILES:

read
  mol pqr molecule.pqr
                                  #complex, protein, ligand
end
ELEC name molecule                                   #complex, protein, ligand

 mg-auto
 dime   161 97 65
 cglen   107.815699 65.201803 45.905097
 fglen   83.421000 58.354002 45.905097
 cgcent 50.416499 45.375001 35.291500
 fgcent 50.416499 45.375001 35.291500
 npbe
 bcfl sdh
 pdie 2.000000
 sdie 80.000000
 chgm spl2
 mol 1
 srfm smol
 srad 1.4
 swin 0.3
 temp 300.00
 sdens 10.0
 calcenergy total
 calcforce no
 write pot dx molecule
                                   #complex, protein, ligand
end
 print elecEnergy molecule
end                      #complex, protein, ligand
quit

SINGLE INPUT FILE:

read
  mol pqr complex.pqr
  mol pqr protein.pqr
  mol pqr ligand.pqr
end
ELEC name complex

 mg-auto
 dime   161 97 65
 cglen   107.815699 65.201803 45.905097
 fglen   83.421000 58.354002 45.905097
 cgcent 50.416499 45.375001 35.291500
 fgcent 50.416499 45.375001 35.291500
 npbe
 bcfl sdh
 pdie 2.000000
 sdie 80.000000
 chgm spl2
 mol 1
 srfm smol
 srad 1.4
 swin 0.3
 temp 300.00
 sdens 10.0
 calcenergy total
 calcforce no
 write pot dx complex

end
ELEC name protein
 mg-auto
 dime   161 97 65
 cglen   107.815699 65.201803 45.905097
 fglen   83.421000 58.354002 45.905097
 cgcent 50.416499 45.375001 35.291500
 fgcent 50.416499 45.375001 35.291500
 npbe
 bcfl sdh
 pdie 2.000000
 sdie 80.000000
 chgm spl2
 mol 1
 srfm smol
 srad 1.4
 swin 0.3
 temp 300.00
 sdens 10.0
 calcenergy total
 calcforce no
 write pot dx protein

end
ELEC name ligand
 mg-auto
 dime   161 97 65
 cglen   107.815699 65.201803 45.905097
 fglen   83.421000 58.354002 45.905097
 cgcent 50.416499 45.375001 35.291500
 fgcent 50.416499 45.375001 35.291500
 npbe
 bcfl sdh
 pdie 2.000000
 sdie 80.000000
 chgm spl2
 mol 1
 srfm smol
 srad 1.4
 swin 0.3
 temp 300.00
 sdens 10.0
 calcenergy total
 calcforce no
 write pot dx ligand

end
 print elecEnergy complex - protein - ligand end
quit


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