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Amber Reference Manuals

There is now one combined Amber reference manual:

Older versions of the manuals are here in Acrobat (PDF) format:

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 266 has now been published.

[266] 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 267 has now been published.

[267] Salomon-Ferrer, R.; Goetz, A. W; Poole, D.; Le Grand, S.; Walker, R. C. Routine microsecond molecular dynamics simulations with AMBER - Part 2: Particle Mesh Ewald, J. Chem. Theo. Comp., 2013,in press, DOI:10.1021/ct400314y

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. 229 In the datafile noxcol cpptraj command example, the last line is incorrect and should read:

datafile phipsi.dat noxcol

p. 241 The avgcoord cpptraj command is deprecated; its functionality is handled by the vector center command (see vector on p. 266).
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. 270 The hist cpptraj command in the example is using old syntax. In AmberTools 13 hist syntax, commas should be used to separate the min/max/step/bins arguments instead of colons. The command should read:

hist phi,-180,180,*,72 psi,-180,180,*,72 out hist.gnu

p. 278 The 'relax' keyword in the ired cpptraj command should be given in MHz, not Hz.
p. 373 "It currently does NOT load decomposition data into available data structures" is untrue -- the MMPBSA.py Python API does load decomposition data into data arrays.