Amber12 and AmberTools13 Reference Manuals

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Amber12 Reference Manual Additions and Corrections

p. 18 Additional information for ntx option:
"Note that NetCDF restart files are automatically detected and are only affected by ntx = 1 or ntx = 5."

p. 19 Additional option for ntxo:
= 2 NetCDF Restart file.

p. 232 The description for ifit should read: Perform rigid fitting before simulation when ifit>0. (One would do this when the initial coordinates for the simulation don't match the coordinates of the map.) When the fit is performed, the map is transformed (by translation and rotation) to match the coordinates; the coordinates are not altered. In addition, EMAP allows output of the re-oriented map (mapfit=...) that matches the (final) simulation coordinates, and/or output of the coordinates (molfit=...) that would match the orientation of the original map. Also: the gammamap variable is in the &cntrl namelist, not in the &emap namelist.

p. 281 Reference 265 has now been published.
[265] Goetz, Andreas W; Williamson, Mark J; Xu, Dong; Poole, Duncan; Grand, Scott Le; Walker, Ross C. Routine microsecond molecular dynamics simulations with amber - part i: Generalized born", J. Chem. Theo. Comp., 2012, 8 (5), pp 1542-1555, DOI:10.1021/ct200909j

p. 281 Reference 585 has now been published.
[585] Skjevik, A.A,; Madej. B.D.; Walker, R.C.; Teigen, K.; "LIPID11: A Modular Framework for Lipid Simulations Using Amber", Journal of Physical Chemistry B, 2012, 116 (36), pp 11124-11136, DOI:10.1021/jp3059992

AmberTools12 Reference Manual Additions and Corrections

p. 22 The instructions five lines from the bottom ("return to step 6") should read "return to the start of step 7."

p. 259-260 The default values for PB variables in MMPBSA.py were updated, but the documentation was not. The variables in bold differ from the manual:
cavity_offset = -0.5692
cavity_surften = 0.0378
exdi = 80.0
fillratio = 4.0
indi = 1.0
inp = 2
istrng = 0.0
linit = 1000
prbrad = 1.4
radiopt = 1
sander_apbs = 0
scale = 2.0

p. 523 Please ignore the section on making parallel ptraj: ptraj.MPI will not be produced using the instructions given in Section A.7.

AmberTools13 Reference Manual Additions and Corrections

p. 244 In the cpptraj diffusion command <filename_root>_a.xmgr is the 'Total distance travelled', and <filename_root>_r.xmgr is the 'Average mean squared displacement'.

p. 18	Additional information for ntx option: "Note that NetCDF restart files are automatically detected and are only affected by ntx = 1 or ntx = 5."
p. 19	Additional option for ntxo: = 2 NetCDF Restart file.
p. 232	The description for ifit should read: Perform rigid fitting before simulation when ifit>0. (One would do this when the initial coordinates for the simulation don't match the coordinates of the map.) When the fit is performed, the map is transformed (by translation and rotation) to match the coordinates; the coordinates are not altered. In addition, EMAP allows output of the re-oriented map (mapfit=...) that matches the (final) simulation coordinates, and/or output of the coordinates (molfit=...) that would match the orientation of the original map. Also: the gammamap variable is in the &cntrl namelist, not in the &emap namelist.
p. 281	Reference 265 has now been published. [265] Goetz, Andreas W; Williamson, Mark J; Xu, Dong; Poole, Duncan; Grand, Scott Le; Walker, Ross C. Routine microsecond molecular dynamics simulations with amber - part i: Generalized born", J. Chem. Theo. Comp., 2012, 8 (5), pp 1542-1555, DOI:10.1021/ct200909j
p. 281	Reference 585 has now been published. [585] Skjevik, A.A,; Madej. B.D.; Walker, R.C.; Teigen, K.; "LIPID11: A Modular Framework for Lipid Simulations Using Amber", Journal of Physical Chemistry B, 2012, 116 (36), pp 11124-11136, DOI:10.1021/jp3059992

p. 22	The instructions five lines from the bottom ("return to step 6") should read "return to the start of step 7."
p. 259-260	The default values for PB variables in MMPBSA.py were updated, but the documentation was not. The variables in bold differ from the manual: cavity_offset = -0.5692 cavity_surften = 0.0378 exdi = 80.0 fillratio = 4.0 indi = 1.0 inp = 2 istrng = 0.0 linit = 1000 prbrad = 1.4 radiopt = 1 sander_apbs = 0 scale = 2.0
p. 523	Please ignore the section on making parallel ptraj: ptraj.MPI will not be produced using the instructions given in Section A.7.