Re: [apbs-users] binding energy calculation dime, cglen and fglen options

[Baker, N. <Nat...@pn...>]

Hello –

The short answer to your question is “no” – because the self-energies need to be subtracted from the total energy by using the same grid locations and spacings for each calculation.

Thanks,

--
Nathan Baker
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling
Pacific Northwest National Laboratory
+1-509-375-3997
http://www.linkedin.com/in/nathanandrewbaker/

From: Cesar Millan [mailto:pac...@gm...]
Sent: Friday, February 28, 2014 6:51 AM
To: apb...@go...
Subject: [apbs-users] binding energy calculation dime, cglen and fglen options

Hi all, sorry for this (probable) naive question. I was looking at the script detailed on http://www.poissonboltzmann.org/apbs/examples/binding-energies/ionic-strength-dependence-of-peptide-rna-interactions and I noted that it uses the same dime, cglen and fglen values for all the system (I suppose that is based on the complex size). The final number print energy complex - peptide - rna end is the binding energy, so the binding energy is in context of the position of the molecules on the complex. My question is, If I determine the dime, cglen and fglen values for each component and run a similar script, Do I have to obtain a equivalent binding energy?

Thank you for any insight that you could provide,

Best regards.

Cesar

   read
       mol pqr model_outNB.pqr
       mol pqr model_outNpep.pqr
       mol pqr model_outBoxB19.pqr
   end
   elec name complex
       mg-auto
       dime 65 97 129
       cglen 45.3322 54.9498 82.2633
       fglen 45.3322 52.3234 68.3902
       cgcent mol 1
       fgcent mol 1
       mol 1
       npbe
       bcfl sdh
       pdie 4.0
       ion charge 1 conc 0.225 radius 2.0
       ion charge -1 conc 0.225 radius 2.0
       sdie 80.0
       srfm mol
       chgm spl2
       sdens 10.00
       srad 1.40
       swin 0.30
       temp 298.15
       calcenergy total
       calcforce no
   end
   elec name peptide
       mg-auto
       dime 65 97 129
       cglen 45.3322 54.9498 82.2633
       fglen 45.3322 52.3234 68.3902
       cgcent mol 1
       fgcent mol 1
       mol 2
       npbe
       bcfl sdh
       pdie 4.0
       sdie 80.0
       ion charge 1 conc 0.225 radius 2.0
       ion charge -1 conc 0.225 radius 2.0
       srfm mol
       chgm spl2
       sdens 10.00
       srad 1.40
       swin 0.30
       temp 298.15
       calcenergy total
       calcforce no
   end
   elec name rna
       mg-auto
       dime 65 97 129
       cglen 45.3322 54.9498 82.2633
       fglen 45.3322 52.3234 68.3902
       cgcent mol 1
       fgcent mol 1
       mol 3
       npbe
       bcfl sdh
       pdie 4.0
       sdie 80.0
       ion charge 1 conc 0.225 radius 2.0
       ion charge -1 conc 0.225 radius 2.0
       srfm mol
       chgm spl2
       sdens 10.00
       srad 1.40
       swin 0.30
       temp 298.15
       calcenergy total
       calcforce no
   end
   print energy complex - peptide - rna end
   quit