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:pachequin@gmail.com]
Sent: Friday, February 28, 2014 6:51 AM
To: apbs-users@googlegroups.com
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