Python wrapper for high-throughput molecular dynamics. A workflow overview and application of MDFit to a data set of macrocyclic peptides targetting PD-L1 are discussed in TBD.1
MDFit currently uses Schrodinger tools. Implementation of alternatives, including open-source tools, are ongoing.
MDFit assumes the $SCHRODINGER
environmental variable has been set. This should point to the current Schrodinger installation. To check if $SCHRODINGER
has been set correctly, try running: $SCHRODINGER/run -h
MDFit attempts to get the current Schrodinger release by reading the $SCHRODINGER
pathname. For example, if the current release is installed in /schrodinger/2023-2/
, MDFit will set the release to 2023-2. This value can also be hard-coded in MDFit (line 38) if a different directory naming scheme is used.
The first time MDFit.py is called, a parameters_TEMPLATE.json
file is generated in the installation directory. Replace localhost
with your institution's Schrodinger hostnames and rename the file to parameters.json
. This is required only once and MDFit will always read parameters.json
to get host information on subsequent runs. General runtime limit guidance:
FFBUILDER 10 hours
BMIN 2 hours
MULTISIM 2 hours
DESMOND 24 hours
ANALYSIS 8 hours
$SCHRODINGER/run python3 MDFit.py -h
Self-contained example available in MDFit/Examples/PDL1/
. The following command will run FFBuilder, three repetitions of 100 ns Desmond MD, and MD analysis for Pep-01, Pep-41, Pep-52, and Pep-66. The first 100 frames will be removed from the trajectory before analysis (--slice_start
) and the cutoff for retaining a protein-ligand interaction is 0.3 (--analysis_cutoff
).
$SCHRODINGER/run python3 MDFit.py -p 6PV9_PDL1.mae -l MDFit_PDL1_Example_Ligands.mae -o "MDFit/Examples/PDL1/PDL1_oplsdir" -t 100000 -r 3 --slice_start 100 --analysis_cutoff 0.3 -d
It is strongly encouraged to use the debug flag -d
for initial MDFit usage. Errors may occur if packages are not where MDFit expects them to be.
- Schrodinger release relying on installation pathname.
Footnotes
-
Reference TBD โฉ