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updates on README.md
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freeenergylab committed Aug 5, 2024
1 parent 62b9a82 commit 93c8a24
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13 changes: 8 additions & 5 deletions README.md
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Expand Up @@ -56,12 +56,15 @@ module load apbs/3.4.1
5. source $HOME/software/anaconda3/2024.06/bin/activate base
6. conda create --name FEP-SPell-ABFE --clone base
7. conda activate FEP-SPell-ABFE
9. pip install rdkit
10. pip install parmed
11. pip install griddata
12. pip install alchemlyb
8. pip install alchemlyb==2.3.1
9. pip install gridDataFormats==1.0.2
10. pip install loguru==0.7.2
11. pip install mrcfile==1.5.3
12. pip install parmed==4.2.2
13. pip install pymbar==4.0.3
14. pip install rdkit==2024.3.3
or, you can also create `FEP-SPell-ABFE` environment using `environment_abfe_yml` file, like:
6-12. conda env create --name FEP-SPell-ABFE --file=environment_abfe.yml
6-14. conda env create --name FEP-SPell-ABFE --file=environment_abfe.yml
###############################################################################
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7 changes: 2 additions & 5 deletions abfe/md/charge_correction.py
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Expand Up @@ -18,10 +18,7 @@
import pandas as pd
import sys
import time
try:
import griddata # v0.1.0
except ModuleNotFoundError:
import gridData # v1.0.2
import gridData # pip install gridDataFormats==1.0.2
import numpy as np
import parmed as pmd

Expand Down Expand Up @@ -312,7 +309,7 @@ def compute_rip(self, dx_file, net_charge):
The result is in kcal-A^3/mol-e (in AMBER units, not APBS units).
"""
dxfile = griddata.Grid(dx_file)
dxfile = gridData.Grid(dx_file)
dV = dxfile.delta.prod()
V = dxfile.grid.size*dV
# Label this as B for box integral, X because it refers to the system X.
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4 changes: 2 additions & 2 deletions environment_abfe.yml
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Expand Up @@ -502,9 +502,9 @@ dependencies:
- zstandard=0.22.0=py312h2c38b39_0
- zstd=1.5.5=hc292b87_2
- pip:
- griddata==0.1.0
- griddataformats==1.0.2
- loguru==0.7.2
- mrcfile==1.5.3
- parmed==4.2.2
- pymbar==4.0.3
- rdkit==2024.3.3
- alchemlyb==2.3.1
4 changes: 2 additions & 2 deletions testing/abfe_testing/dG_components_results.csv
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@@ -1,4 +1,4 @@
,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic
phn,5.27,0.00,5.22,0.00,4.60,0.00,-8.37,9.58,4.58,0.00,-8.77,9.58
phn,5.20,0.00,5.16,0.00,9.72,0.00,-5.57,9.64,9.70,0.00,-6.27,9.64
,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic
bnz,1.13,0.00,1.06,0.00,6.25,0.00,-7.06,9.60,6.25,0.00,-7.62,9.60
bnz,1.19,0.00,1.14,0.00,7.15,0.00,-6.72,9.58,7.06,0.00,-7.33,9.58
4 changes: 2 additions & 2 deletions testing/abfe_testing/dG_results.csv
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@@ -1,4 +1,4 @@
,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std
phn,1.88,0.07,1.46,0.08
phn,-0.45,0.06,-1.16,0.09
,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std
bnz,-2.59,0.06,-3.21,0.07
bnz,-3.11,0.06,-3.67,0.07

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