[apbs-users] APBS Positive Salvation Energy

[Cooper, Sarah Jane]

Hello,

I’m currently trying to use APBS to generate PMFs that match some MD data but the PMF’s I’m getting from adding the polar and nonpolar components using a modified version of the Run_membrane_helix script captures the overall shape but the resulting are positive not negative as they should be so the APBS PMF’s are basically upside down. The membrane includes head groups as well with a dielectric constant of 10. Apolar calculations use values similar to that of the alkanes example with CHARMM parameters and seem to make sense. I suspect this problem has something to do with the polar calculations. These are small molecules so the protein dielectric is set to 1. Input files are below. 

dummy_calc.in

#zmem -20.0

#lmem 40.0

#mdie 2.0

#idie 10.0

#geo1 0.0

#geo2 0.0

#geo3 7.0

READ

   mol pqr MOL.pqr

END

ELEC name solv0

   mg-dummy

   dime 257 257 257

   glen 200 200 200

   lpbe

   pdie 1.0

   sdie 80.0

   bcfl zero

   ion

   charge 1.0

   conc 0.15

   radius 2.0

   ion

   charge -1.0

   conc 0.15

   radius 2.0

   gcent 0 0 0

   mol 1

   chgm spl2

   srfm mol

   srad 0.6

   swin 0.3

   sdens 10.0

   temp 298.15

   calcenergy no

   calcforce no

   write dielx dx dielx_1

   write diely dx diely_1

   write dielz dx dielz_1

   write kappa dx kappa_1

   write charge dx charge_1

END

QUIT

dummy_calc.in

#APBSmem parameters and geometric factors

#zmem -20.0

#lmem 40.0

#mdie 2.0

#idie 10.0

#geo1 0.0

#geo2 0.0

#geo3 7.0

READ

   # mol pqr file for polar calc

   mol pqr MOL.pqr

   # read maps for polar calc

   diel dx dielx_1m.dx diely_1m.dx dielz_1m.dx

   kappa dx kappa_1m.dx

   charge dx charge_1m.dx

END

ELEC name solv0

   mg-manual

   dime 257 257 257

   glen 200 200 200

   lpbe

   pdie 1.0

   sdie 80.0

   bcfl zero

   ion

   charge 1.0

   conc 0.15

   radius 2.0

   ion

   charge -1.0

   conc 0.15

   radius 2.0

   gcent 0 0 0

   mol 1

   chgm spl2

   srfm mol

   srad 0.6

   swin 0.3

   sdens 10.0

   temp 298.15

   calcenergy total

   calcforce no

   write pot dx pot_1

END

ELEC name ref0

   mg-manual

   dime 257 257 257

   glen 200 200 200

   lpbe

   pdie 1.0

   sdie 80.0

   bcfl zero

   ion

   charge 1.0

   conc 0.15

   radius 2.0

   ion

   charge -1.0

   conc 0.15

   radius 2.0

   gcent 0 0 0

   mol 1

   chgm spl2

   srfm mol

   srad 0.6

   swin 0.3

   sdens 10.0

   temp 298.15

   calcenergy total

   calcforce no

   usemap diel 1

   usemap kappa 1

   usemap charge 1

   write pot dx pot_1

END

PRINT elecEnergy ref0 - solv0 END

QUIT

Any help/thoughts are much appreciated.

Thanks!

Sarah

[Nathan Baker]

Hi Sarah –

 

I’m Cc’ing Michael Grabe (developer of APBSmem) for his help.

 

Thanks,

Nathan

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