The example input files in this directory calculate nonpolar solvation energies for alkanes based on the protocol described in Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006. (http://dx.doi.org/10.1073/pnas.0600118103).
This example was contributed by Nathan Baker and Jason Wagoner.
Output files are generated and executed by the runme.sh script.
APBS Version | Alkane | SASA (Å2) | SASA energy (kJ/mol) | SAV (Å3) | SAV energy (kJ/mol) | WCA energy (kJ/mol) | Total nonpolar solvation energy (kJ/mol) |
---|---|---|---|---|---|---|---|
1.2.1 | 2-methylbutane | 214.202 | 1.82072 | 253.906 | 60.7852 | -48.3035 | 1.439739455792E+01 |
butane | 193.855 | 1.64777 | 218.119 | 52.2176 | -41.6443 | 1.208346456826E+01 | |
cyclohexane | 221.799 | 1.88529 | 267.165 | 63.9593 | -52.4787 | 1.354016672221E+01 | |
cyclopentane | 193.638 | 1.64593 | 218.412 | 52.2877 | -44.3607 | 9.363673200142E+00 | |
ethane | 139.427 | 1.18513 | 140.692 | 33.6818 | -25.4382 | 9.422717598546E+00 | |
hexane | 250.291 | 2.12748 | 297.703 | 71.2701 | -57.1544 | 1.640068943201E+01 | |
isobutane | 192.744 | 1.63832 | 219.153 | 52.4652 | -40.8617 | 1.323144287435E+01 | |
methane | 105.42 | 0.896066 | 95.4242 | 22.8446 | -15.9414 | 7.894367190329E+00 | |
neopentane | 210.755 | 1.79141 | 251.314 | 60.1647 | -47.4807 | 1.449633815052E+01 | |
pentane | 222.524 | 259.149 | 1.89145 | 62.0403 | -49.456 | 1.447900211546E+01 | |
propane | 170.391 | 182.703 | 1.44832 | 43.739 | -33.4629 | 1.192358496286E+01 |
APBS Version | Alkane | SASA (Å2) | SASA energy (kJ/mol) | SAV (Å3) | SAV energy (kJ/mol) | WCA energy (kJ/mol) | Total nonpolar solvation energy (kJ/mol) |
---|---|---|---|---|---|---|---|
1.2 | 2-methylbutane | 214.202 | 1.82072 | 253.906 | 60.7852 | -48.3035 | 1.439739455792E+01 |
butane | 193.855 | 1.64777 | 218.119 | 52.2176 | -41.6443 | 1.208346456826E+01 | |
cyclohexane | 221.799 | 1.88529 | 267.165 | 63.9593 | -52.4787 | 1.354016672221E+01 | |
cyclopentane | 193.638 | 1.64593 | 218.412 | 52.2877 | -44.3607 | 9.363673200142E+00 | |
ethane | 139.427 | 1.18513 | 140.692 | 33.6818 | -25.4382 | 9.422717598546E+00 | |
hexane | 250.291 | 2.12748 | 297.703 | 71.2701 | -57.1544 | 1.640068943201E+01 | |
isobutane | 192.744 | 1.63832 | 219.153 | 52.4652 | -40.8617 | 1.323144287435E+01 | |
methane | 105.42 | 0.896066 | 95.4242 | 22.8446 | -15.9414 | 7.894367190329E+00 | |
neopentane | 210.755 | 1.79141 | 251.314 | 60.1647 | -47.4807 | 1.449633815052E+01 | |
pentane | 222.524 | 259.149 | 1.89145 | 62.0403 | -49.456 | 1.447900211546E+01 | |
propane | 170.391 | 182.703 | 1.44832 | 43.739 | -33.4629 | 1.192358496286E+01 |
APBS Version | Alkane | SASA (Å2) | SASA energy (kJ/mol) | SAV (Å3) | SAV energy (kJ/mol) | WCA energy (kJ/mol) | Total nonpolar solvation energy (kJ/mol) |
---|---|---|---|---|---|---|---|
1.1.0 | 2-methylbutane | 214.202 | 1.82072 | 253.906 | 60.7852 | -48.3035 | 1.439739455792E+01 |
butane | 193.855 | 1.64777 | 218.119 | 52.2176 | -41.6443 | 1.208346456826E+01 | |
cyclohexane | 221.799 | 1.88529 | 267.165 | 63.9593 | -52.4787 | 1.354016672221E+01 | |
cyclopentane | 193.638 | 1.64593 | 218.412 | 52.2877 | -44.3607 | 9.363673200142E+00 | |
ethane | 139.427 | 1.18513 | 140.692 | 33.6818 | -25.4382 | 9.422717598546E+00 | |
hexane | 250.291 | 2.12748 | 297.703 | 71.2701 | -57.1544 | 1.640068943201E+01 | |
isobutane | 192.744 | 1.63832 | 219.153 | 52.4652 | -40.8617 | 1.323144287435E+01 | |
methane | 105.42 | 0.896066 | 95.4242 | 22.8446 | -15.9414 | 7.894367190329E+00 | |
neopentane | 210.755 | 1.79141 | 251.314 | 60.1647 | -47.4807 | 1.449633815052E+01 | |
pentane | 222.524 | 259.149 | 1.89145 | 62.0403 | -49.456 | 1.447900211546E+01 | |
propane | 170.391 | 182.703 | 1.44832 | 43.739 | -33.4629 | 1.192358496286E+01 |
APBS Version | Alkane | SASA (Å2) | SASA energy (kJ/mol) | SAV (Å3) | SAV energy (kJ/mol) | WCA energy (kJ/mol) | Total nonpolar solvation energy (kJ/mol) |
---|---|---|---|---|---|---|---|
1.0.0 | 2-methylbutane | 214.202 | 1.82072 | 253.906 | 60.7852 | -48.3035 | 1.439739455792E+01 |
butane | 193.855 | 1.64777 | 218.119 | 52.2176 | -41.6443 | 1.208346456826E+01 | |
cyclohexane | 221.799 | 1.88529 | 267.165 | 63.9593 | -52.4787 | 1.354016672221E+01 | |
cyclopentane | 193.638 | 1.64593 | 218.412 | 52.2877 | -44.3607 | 9.363673200142E+00 | |
ethane | 139.427 | 1.18513 | 140.692 | 33.6818 | -25.4382 | 9.422717598546E+00 | |
hexane | 250.291 | 2.12748 | 297.703 | 71.2701 | -57.1544 | 1.640068943201E+01 | |
isobutane | 192.744 | 1.63832 | 219.153 | 52.4652 | -40.8617 | 1.323144287435E+01 | |
methane | 105.42 | 0.896066 | 95.4242 | 22.8446 | -15.9414 | 7.894367190329E+00 | |
neopentane | 210.755 | 1.79141 | 251.314 | 60.1647 | -47.4807 | 1.449633815052E+01 | |
pentane | 222.524 | 259.149 | 1.89145 | 62.0403 | -49.456 | 1.447900211546E+01 | |
propane | 170.391 | 182.703 | 1.44832 | 43.739 | -33.4629 | 1.192358496286E+01 |
APBS Version | Alkane | SASA (Å2) | SASA energy (kJ/mol) | SAV (Å3) | SAV energy (kJ/mol) | WCA energy (kJ/mol) | Total nonpolar solvation energy (kJ/mol) |
---|---|---|---|---|---|---|---|
0.5.11 | 2-methylbutane | 214.202 | 1.82072 | 253.906 | 60.7852 | -48.3035 | 1.439739455792E+01 |
butane | 193.855 | 1.64777 | 218.119 | 52.2176 | -41.6443 | 1.208346456826E+01 | |
cyclohexane | 221.799 | 1.88529 | 267.165 | 63.9593 | -52.4787 | 1.354016672221E+01 | |
cyclopentane | 193.638 | 1.64593 | 218.412 | 52.2877 | -44.3607 | 9.363673200142E+00 | |
ethane | 139.427 | 1.18513 | 140.692 | 33.6818 | -25.4382 | 9.422717598546E+00 | |
hexane | 250.291 | 2.12748 | 297.703 | 71.2701 | -57.1544 | 1.640068943201E+01 | |
isobutane | 192.744 | 1.63832 | 219.153 | 52.4652 | -40.8617 | 1.323144287435E+01 | |
methane | 105.42 | 0.896066 | 95.4242 | 22.8446 | -15.9414 | 7.894367190329E+00 | |
neopentane | 210.755 | 1.79141 | 251.314 | 60.1647 | -47.4807 | 1.449633815052E+01 | |
pentane | 222.524 | 259.149 | 1.89145 | 62.0403 | -49.456 | 1.447900211546E+01 | |
propane | 170.391 | 182.703 | 1.44832 | 43.739 | -33.4629 | 1.192358496286E+01 |
APBS Version | Alkane | SASA (Å2) | SASA energy (kJ/mol) | SAV (Å3) | SAV energy (kJ/mol) | WCA energy (kJ/mol) | Total nonpolar solvation energy (kJ/mol) |
---|---|---|---|---|---|---|---|
0.5.0 | 2-methylbutane | 214.202 | 1.82072 | 253.906 | 60.7852 | -48.3035 | 1.430239579640E+01 |
butane | 193.855 | 1.64777 | 218.119 | 52.2176 | -41.6443 | 1.222110127537E+01 | |
cyclohexane | 221.799 | 1.88529 | 267.165 | 63.9593 | -52.4787 | 1.336586748209E+01 | |
cyclopentane | 193.638 | 1.64593 | 218.412 | 52.2877 | -44.3607 | 9.572911268235E+00 | |
ethane | 139.427 | 1.18513 | 140.692 | 33.6818 | -25.4382 | 9.428701470984E+00 | |
hexane | 250.291 | 2.12748 | 297.703 | 71.2701 | -57.1544 | 1.624316652259E+01 | |
isobutane | 192.744 | 1.63832 | 219.153 | 52.4652 | -40.8617 | 1.324178842307E+01 | |
methane | 105.42 | 0.896066 | 95.4242 | 22.8446 | -15.9414 | 7.799212389992E+00 | |
neopentane | 210.755 | 1.79141 | 251.314 | 60.1647 | -47.4807 | 1.447540747648E+01 | |
pentane | 222.524 | 259.149 | 1.89145 | 62.0403 | -49.456 | 1.447574303821E+01 | |
propane | 170.391 | 182.703 | 1.44832 | 43.739 | -33.4629 | 1.172438897305E+01 |
1 The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):