Simulation of Diffusional Association
(version 6)
SDA
example
run "bnbs-apbs"
This example run can be found in
examples/bnbs-apbs.
The following subdirectories are present in this directory :
Barnase and barstar association example
The results of SDA run can be found in run-hits/ subdirectory or can be generated in a new run/ subdirectory using the script scr/bnbs-apbs-prepare-and-run . In order to execute this script locally, you need to define 2 parameters - the location ofi the SDA6 distribution directory and the location of the APBS executable.
2 types of simulation are done in this example: simulations without the non-polar desolvation term (similar to ones done with SDA version 4) and simulations with a weak non-polar desolvation term (with the proportionality factor of 13 cal/mole per 1 Å2 buried surface area).
Simulations with (only) electrostatic terms reproduce the experimental association rate when the formation of 2 contacts at ~6Å is used as the criterion for formation of an encounter complex. Simulations with the weak non-polar term included result in formation of encounter complex at a ca 10 times higher rate at a range of contact distances and the number of contacts. Namely, 3 or 4 contacts are formed at the same rate with contact distances from 4 to 10 Å. At contact distances ~ 4 Å, formation of 2, 3 or 4 contacts occurs at the same rate.
The results are similar (but not identical) to the barnase and barstar association example using UHBD (see examples/bnbs ). PQR files are used in this APBS example, while in the UHBD example, a combination of pdb files with and without hydrogens and a qtable are used in order to reproduce the original simulation results [Gabdoulline RR and Wade RC. Simulation of the Diffusional Association of Barnase and Barstar. Biophys. J. (1997) 72, 1917-1929. (Abstract)]. The differences are listed in the following table:
The following subdirectories are present in this directory :
| run-hits/ | Results of the example run
script
for barnase and barstar association at HITS |
| data/
|
Data files (pdb and input files)
needed for running the barnase and barstar example |
| doc/ |
Documentation |
| scr/ |
Scripts to do the example run |
Barnase and barstar association example
The results of SDA run can be found in run-hits/ subdirectory or can be generated in a new run/ subdirectory using the script scr/bnbs-apbs-prepare-and-run . In order to execute this script locally, you need to define 2 parameters - the location ofi the SDA6 distribution directory and the location of the APBS executable.
2 types of simulation are done in this example: simulations without the non-polar desolvation term (similar to ones done with SDA version 4) and simulations with a weak non-polar desolvation term (with the proportionality factor of 13 cal/mole per 1 Å2 buried surface area).
Simulations with (only) electrostatic terms reproduce the experimental association rate when the formation of 2 contacts at ~6Å is used as the criterion for formation of an encounter complex. Simulations with the weak non-polar term included result in formation of encounter complex at a ca 10 times higher rate at a range of contact distances and the number of contacts. Namely, 3 or 4 contacts are formed at the same rate with contact distances from 4 to 10 Å. At contact distances ~ 4 Å, formation of 2, 3 or 4 contacts occurs at the same rate.
Residence times
are calculated afterwards using sda-koff.
A typical result looks
like this:
With the non-polar term,
complexes defined by 2,3 or 4 contacts at contact
distances
of 6-10 Å are maintained for ca. 50 ns, i.e. ca. 1000 times
longer
than in the absence of the non-polar term.
The results are similar (but not identical) to the barnase and barstar association example using UHBD (see examples/bnbs ). PQR files are used in this APBS example, while in the UHBD example, a combination of pdb files with and without hydrogens and a qtable are used in order to reproduce the original simulation results [Gabdoulline RR and Wade RC. Simulation of the Diffusional Association of Barnase and Barstar. Biophys. J. (1997) 72, 1917-1929. (Abstract)]. The differences are listed in the following table:
| Example run using APBS |
Example run using UHBD |
|
| Charge assignment and
electrostatic calculations |
AMBER charges are assigned using
pdb2pqr, generating a file with all hydrogens and electrostatic potentials are calculated with APBS and
converted to UHBD format with apbs2uhbd. The grid has 129^3 points. |
OPLS charges are assigned using
data/qtable.dat with only polar hydrogens present and electrostatic potentials are calculated with UHBD.
The grid has 150^3 points. |
| Effective charge sites |
The pqr file has no CTRM and NTRM residues,
although they are charged in electrostatic potential
calculations. These effective charge sites have to be generated using an appropriate pdb file (with renamed residues - p*-noh.pdb) or inserted to *.tcha files before ecm
calculations. |
CTRM and NTRM in the pdb file (p*_polarh.pdb/p*_noh.pdb) are recognized
by ecm_mksites andi the appropriate atoms are defined as charge sites. |