This example shows how to use the DT-Grid data structure in potential of mean force (PMF) calculations for compression of Lennard-Jones (LJ) potential grids.
The compatibility with DT-Grid structures and files has been implemented in SDA 7 mostly for application to the short-range interactions of large macromolecules. In this simple example, however, it will be used for compression of the LJ potential of the three-histidine (3HIS) tripeptide for computing the PMF of the peptide with an Au(111) surface as shown in the au3his example. Details are given in : Ozboyaci, M., Martinez, M. and Wade, R.C. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.J. Chem. Theory Comput. (2016), 59:7598-7616. 10.1021/acs.jctc.6b00350
This example can be found in directory examples/au3his/.
| prepare_grids_and_ecm/ | Directory for generating grids and effective charges needed for running the simulation |
| data_grid/ | Data files (pdb and input files) needed for running the examples |
| run_dtgrid_hits/ | Results of the example run script for protein-metal surface docking using DT-Grid |
| run_dtgrid/ | Directory to run the DT-Grid file conversion and the PMF calculations |
| doc/ | This documentation |
Please see the au3his example and the input pages for the descriptions of the parameters.
Assure you have compiled all the executables and tools in sda_flex/bin/ first or refer to the compilation section.
If you have not gone through the au3his example before, run the script run-au3his_ed_hd_ecm_lj.sh from the prepare_grids_and_ecm/ directory to generate all the regular grids necessary for this example.
Then go into the run_dtgrid/ directory that contains the input file and run the shell script:
cd run_dtgrid/
./run_sda_dtgrid.sh
Ensure that the output files are similar to the ones generated in the *_hits directory.
Alternatively, you can convert the LJ grids in the au3his example from UHBD to DT-Grid file formats using the following commands:
cd ./data_grid/
../../../bin/UHBD2dtgrid -g p2lj1.grd -p p2.pqr -f binary -o p2lj1.dtgrd -s 10.0 -pr 0.0
../../../bin/UHBD2dtgrid -g p2lj2.grd -p p2.pqr -f binary -o p2lj2.dtgrd -s 10.0 -pr 0.0
These commands will create two grid files named: p2lj1.dtgrd and p2lj2.dtgrd.
You can, then, change the grid names in the sda input file for the ljf input parameter, and run the calculations.
In case you delete or lose the original UHBD format grid files and need them later, you can recover them from the DT-Grid format grid files using the following commands:
../../../bin/dtgrid2UHBD -g p2lj1.dtgrd -f binary -o p2lj1.grd
../../../bin/dtgrid2UHBD -g p2lj2.dtgrd -f binary -o p2lj2.grd
Please note that the omitted values during the DT-Grid compression may not be completely recovered!