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I would like to use the charmm CMAP correction in another program (PyRosetta). I have looked at parmfile.doc and io.doc and this discussion, but nowhere is it distinctly written how the CMAP is laid out.

For example:

PHI1 PHI2 PHI3 PHI4 PSI1 PSI2 PSI3 PSI4 24
!-180
1 2 3 …

Is this read as:

PHI PSI E
-180 -180 1
-180 -165 2
-180 -150 3

Or as:

PHI PSI E
-180 -180 1
-165 -180 2
-150 -180 3

Also out of curiosity, must the CMAP be defined between two consecutive torsion angles, or can the angles be far apart (topologically)?

PS: This is crossposted from here. And I must say using UBB forums is a pain after getting used to the wonderful SE interface:)

PPS: Would this Q find a better home at https://scicomp.stackexchange.com/?

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In the latest version of the CHARMM forcefield in par_all36_prot.prm the comments are a bit more informative:

CMAP
! alanine map
C    NH1  CT1  C    NH1  CT1  C    NH1   24
! phi = -180.0
     0.126790      0.768700      0.971260      1.250970      2.121010
     2.720430      2.089440      1.789790 

So from that it can be inferred that my example is read as

PHI PSI E
-180 -180 1
-180 -165 2
-180 -150 3
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