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.
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 :
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 Å; for qualitative, a grid spacing of ~0.5 Å should be OK. Regardless, you should test your results to be sure that your conclusions are not sensitive to the choice of grid spacing.
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).
PDB2PQR will generate an APBS input file for you to use as a starting point.
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?
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).
Does the program does this automatic if i choose mg-auto?
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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