Closed dfhahn closed 3 years ago
Thank you for getting this up @dfhahn! I'll be reviewing this, but we will also seek testing help with Bill. Please let me know when you have set up a call with him to try things out on his infrastructure.
@dfhahn, if I have some time, is this ready for my to try out? Are there particular code segments/commands that I can provide feedback on?
@j-wags , I just pushed some changes. Now it is ready to be tried out! Just try to follow the protocol above and let be know about encountered issues or suggestions for improvements.
This PR has been superseded by #84, which targets a merge into the season-1
branch, so that the schrodinger functionality can continue using the openforcefield
namespace.
Description
This PR introduces the building of custom OPLS3e parameters and optimization of conformers with Schrodinger tools
Installation of
schrodinger
command group in a dev environmentFirst, follow the installation procedures for the
openff-benchmark-optimization
environment described in Deployment Procedure documentOnce this is done, you can clone the environment into a development environment:
Install the
schrodinger
branch from github:Docs
General help about new command group:
openff-benchmark schrodinger --help
General comments
The
schrodinger
command group needs access to Schrodinger binaries. They will try to use the SCHRODINGER environment variable. If it is not set, the path to the Schrodinger binaries can be set in the--schrodinger-path
command line option of the following commands.Additionally, the OPLS3e force field makes use of custom parameters. The custom parameter directory can be set with the
--opls-dir
command line option.The commands
ffbuilder
andoptimize
have the additional options to set--host
and--max-jobs
. With the--host
option, you can specify the host (queue) on which the ffbuilder or optimization should be run. The name of the host has to be specified in your schrodinger.hosts configuration file. With--max-jobs
, you can set the maximal number of parallel subjobs run on the host. If these options are not specified, default settings will be used.Step 1: Build custom parameters
Start up a ffbuilder custom parameter calculation using default arguments and the QM optimized molecules:
openff-benchmark schrodinger ffbuilder [--opls-dir ~/.schrodinger/opls_dir] 4-compute-qm/b3lyp-d3bj/dzvp/
It takes into account already available custom parameters in the path given as the option
--opls-dir
. If--opls-dir
is not given or the specified path is not available (i.e. if you are a new user), all parameters will be calculated from scratch. If you run the ffbuilder for the first time and don't have custom parameters yet, do not specify the--opls-dir
as this will lead to an error. The same counts if you used OPLS3e before and run the ffbuilder for the first time with OPLS4. The command will create a ffbuilder jobffb_openff_benchmark
in the directory7-schrodinger-ffb
. If there are already output files in the output directory, they will be moved to a backup directory7-schrodinger-ffb/ffb_openff_benchmark.bk[.x]
and previously build custom parameters will be automatically merged with the custom parameter path. The output directory can be changed with the-o/--output-path
option.Now you have to wait until the ffbuilder job has finished. You can check the progress of the calculations in the file
7-schrodinger-ffb/ffb_openff_benchmark.log
.Note: You might realize that the ffbuilder input file
ffb_input.sdf
includes less conformers than you gave as an input. That is correct as the ffbuilder needs only one conformer per molecule.Step 2: Merge parameters in custom parameter path
This command merges the newly built parameters to your custom parameter path.
openff-benchmark schrodinger ffmerge 7-schrodinger-ffb
The input path must be the output path of step 1. The custom parameters path can be specified with the option
--opls-dir
, which defaults to~/.schrodinger/opls_dir/
. If the specified or the default--opls-dir
does not exist, the directory will be created and initialized. This could be the case if you are a new user or you want to create a separate custom parameter directory.Step 3a: Run optimization without custom parameters
Optimization using OPLS3e using NO custom parameters:
openff-benchmark schrodinger optimize 4-compute-qm/b3lyp-d3bj/dzvp/
This will create a Schrodinger macromodel optimization run in the directory
8-schrodinger-mm-default
. The latter directory can be changed with the-o/--output-path
option. If the directory already exists and you want to replace the data, you need to run the command with the option--delete-existing
.Step 3b: Run optimization with custom parameters
By adding a custom parameter path to the
optimize
command, the optimization will use OPLS3e with custom parameters. Warning: If you have not built the custom parameters correctly and merged them to your custom parameter path, (steps 1 and 2), the command will use the available custom parameters, but the newly built parameters will be missing.openff-benchmark schrodinger optimize --opls-dir ${HOME}/.schrodinger/opls_dir 4-compute-qm/b3lyp-d3bj/dzvp/
This will create a Schrodinger macromodel optimization run in the directory
9-schrodinger-mm-custom
. The latter directory can be changed with the-o/--output-path
option. If the directory already exists and you want to replace the data, you need to run the command with the option--delete-existing
.Step 4: Postprocessing
The output files
mmod_output.maegz
in the respective directories will be postprocessed with the commands:openff-benchmark schrodinger postprocess -o 4-compute-mm 8-schrodinger-mm-default/mmod_output.maegz
and
openff-benchmark schrodinger postprocess -o 4-compute-mm 9-schrodinger-mm-custom/mmod_output.maegz
This will save the postprocessed SDF files in
4-compute-mm/opls3e_default
or4-compute-mm/opls3e_custom
. If these directories exist already and you want to replace the data, you need to run the commands with the option--delete-existing
.Hint: The last two commands can be run together:
openff-benchmark schrodinger postprocess -o 4-compute-mm 8-schrodinger-mm-default/mmod_output.maegz 9-schrodinger-mm-custom/mmod_output.maegz
)The respective output directories can be included in the final analysis steps.
Todos
ffbuilder
ffbuilder
schrodinger optimize
optimization with Schrodinger macromodelschrodinger postprocess
postprocessing of macromodel outputQuestions
ffbuilder
: Split the calculation up in several subjobs with batches of e.g. 100 molecules? -> This can be done by the user, i.e.will create 10 ffbuilder jobs with batches of 100 molecules for molecules with
molecule_index
from00000
to00999
Status