The following is the directory structure.
HNE directory:
amber-gaff2:
antechamber: ligands mol2, rtf and prm files (original FF charges)
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - MSLD prep and production run files for the water side (ligands with original FF charges)
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - used result from corresponding **PR3** calculations
charmm-cgenff:
cgenff: ligands mol2, rtf and prm files (original FF charges)
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - MSLD prep and production run files for the water side (ligands with original FF charges)
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - MSLD prep and production run files for the water side (hybrid ligands with renormalized charges)
opls-opls:
ligpargen: protein mol2, pdb, rtf and prm files (original FF charges)
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - MSLD prep and production run files for the water side (ligands with original FF charges)
compound_2-10: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - MSLD prep and production run files for the water side (hybrid ligands with renormalized charges)
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - MSLD prep and production run files for the water side (hybrid ligands with renormalized charges)
charmm-opls:
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - MSLD prep and production run files for the water side (ligands with original FF charges)
compound_2-10: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - used result from corresponding **PR3** calculations
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - MSLD prep and production run files for the water side (hybrid ligands with renormalized charges)
PR3 directory:
amber-gaff2:
antechamber: ligands mol2, rtf and prm files (original FF charges)
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - used result from corresponding **HNE** calculations
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - MSLD prep and production run files for the water side (hybrid ligands with renormalized charges)
charmm-cgenff:
cgenff: ligands mol2, rtf and prm files (original FF charges)
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - used result from corresponding **HNE** calculations
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - used result from corresponding **HNE** calculations
opls-opls:
ligpargen: protein mol2, pdb, rtf and prm files (original FF charges)
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - used result from corresponding **HNE** calculations
compound_2-10: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - used result from corresponding **HNE** calculations
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - used result from corresponding **HNE** calculations
charmm-opls:
compound_1-2: protein - MSLD prep and production run files for the complex side (ligands with original FF charges)
water - used result from corresponding **HNE** calculations
compound_2-10: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - MSLD prep and production run files for the water side (hybrid ligands with renormalized charges)
compounds_2-11: protein - MSLD prep and production run files for the complex side (hybrid ligands with renormalized charges)
water - used result from corresponding **HNE** calculations
Charge renormalization was performed using msld_py_prep.
FF - Force Field
ALF - Adaptive Landscape Flattening
-
HNE: CHARMM stream files containing original FF charges and renormalized charges (following charge renormalization).
-
PR3: CHARMM stream files containing original FF charges and renormalized charges (following charge renormalization).
CHARMM input files for book-ending correction, MBAR analysis scripts. see also - msld_py_prep
CHARMM, ALF, and bash scripts for running MSLD simulations.
| Publication | RawData |
|---|---|
| 1 | mol22 |
| 2 | mol46 |
| 3 | mol48 |
| 4 | mol49 |
| 5 | mol50 |
| 6 | mol51 |
| 7 | mol53 |
| 8 | mol54 |
| 9 | mol55 |
| 10 | mol56 |
| 11 | mol58 |