alchemical FEP studies of FOXO1 mutations
For FEP, I used
(1) the default Gromacs: gromacs/2016.3;
(2) I have 30 lambdas (there are 4 different intervals in these 30 lambdas)
0.000 0.002 0.004 0.006 0.008 0.01 0.02 0.03 0.04 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 0.975 1.00
(3) force field: Amber14sbmut
I combine two topologies: one is alchemical topology, the other one is protein-metal topology.
(4) alchemical topology built with pmx Github (Gapsys)
(5) protein-metal topology built with MCPB.py (Li, Pengfei) from Ambertools17.6
(6) There are 3 thermodynamic equations: each production running 1ns.
The pipeline files can be found in FOXO1-fep/FEP/FOXO1_FEP/ folder. There are 3 main_stage*.sh files: main_stage1.sh(top and gro prep), main_stage2.sh(EM), and main_stage3.sh(prep before upload). In main_stage1.sh, 2 pipeline files: pipeline_v1.sh or pipeline_v2.sh can be called and performed. In pipeline_.sh files, different job_.sh and job_*.py files can be called and performed.