Hello --

You can construct a free energy cycle to make either contribution work.  However, if you want to use the analytic version of Coulomb's law, then you need to use a reference state with pdie = sdie.

-- Nathan

On Aug 20, 2009, at 11:51 AM, Tiago Lopes Gomes wrote:


The previous was related to the input file setup, not directly to do with this one. Just to know how to set grid dimensions and another parameters, before i started the calculations.
So it means that to calculate the energy of the reference compound i would have to put pdie=1 and sdie=1, or pdie=2 and sdie=1?
going to check the articles and the user guide for the apolar parts

thanks a lot


I post the previous post here with the answers :

Hello --

i am studying the interaction between a peptide (13 aa) and a protein
( 44 aa), and i would like to compute the binding energy following the
thermodynamic cycle included in the tutorials. A few questions,

How one knows the parameters t use for the calculations namely the
grid dimensions ( grid and dime parameters).

I would use a program like PDB2PQR (http://pdb2pqr.sf.net/) as a starting point.  For quantitative calculations, I would recommend a grid spacing of less than 0.5 ; for qualitative, a grid spacing of ~0.5 should be OK.  Regardless, you should test your results to be sure that your conclusions are not sensitive to the choice of grid spacing.

Which apbs.in shall i use from the examples directory. Does one need to use the psize.py to do
this automatic, like in the GUI. If yes how?

PDB2PQR will generate an APBS input file for you to use as a starting point.

Does the program does this automatic if i choose mg-auto?

No, I would recommend reading the documentation at http://apbs.wustl.edu/ and pay particular attention to the ELEC section (http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section).

Good luck,


I tried also different force fields in generating pqr files (Amber and
Parse), with different results, i guess is is normal, i don't know
what is the most appropriate forcefield ( maybe depends on the system

If i missed any tutorial pleased point me to it.


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