How to calculate surface electrostatics using MD DaVis?

Delphi and MSMS must be installed for this to work. You may download these from: Delphi and MSMS

You will need the parameter files for delphi run, which can be downloaded from paramter files

Step 1: Calculate the electrostatics using the following command

md_davis electrostatics --surface_potential \
    -m ~/.opt/msms/ \
    -d ~/.opt/delphi8.4.2_sequential
    -c path/to/charge/file.crg \
    -r path/to/radius/file.siz \
    PDB_FILE.pdb \
    path/to/electrostatics/output/directory

The following charge and radius files are provided with the source code for MD DaVis.

md_davis/md_davis/electrostatics/charmm.crg
md_davis/md_davis/electrostatics/charmm.siz

If you receive a warning during Delphi run regarding missing charge or radius. Then the missing properties must be added to these files or whichever files you provide to md_davis electrostatics.

Step 2: Add the surface electrostatics data into the residue dataframe by modifying the command for creating residue dataframe to include the option -d and specifying the path to the directory containing the surface potential files. This will search for all .pot files and include their mean and total in the residue dataframe.

md_davis residue dataframe \
        --potential  path/to/electrostatics/output/directory \
        --annotation  annotations.json \
        --prefix  prefix \
        md_davis_collect_output_data.h5  \
        output_residue_wise_data.p

Step 3: Plot the residue dataframe with the usual command:

md_davis plot residue output_residue_wise_data.p