Dear Amber developers,
I wanted to compute energy functions for protein conformations
simulated with pmemd.cuda + chamber topology file.
I found that cpptraj includes codes for the energy calculations
(Action_Energy.cpp and Energy.cpp), but they cannot be used
with chamber topology to compute charmm-specific energy terms.
It was not difficult to add a new action code to compute the
Urey-Bradley, improper torsion, and CMAP terms using the
public members of the class ChamberParmType in ParameterTypes.h,
and this could be done without touching any of the original cpptraj codes.
However, I had difficulty in computing the 1-4 LJ term.
(1-4 LJ parameters for certain atom pairs are different from
normal LJ parameters in charmm.)
LJ14() is included in ChamberParmType, but this is not updated
when topology is modified (e.g., stripping), and it is nicer if the function
like GetLJparam is also available for 1-4 LJ parameters.
For this reason, I had to modify some parts of the original cpptraj codes
(e.g., Topology.cpp) to compute the 1-4 LJ energy, but I wanted to
avoid this since this will cause problems in future updates.
I don't know whether there is such general demand ... but
I would appreciate it very much if cpptraj is updated in future
such that it can compute energy with chamber topology
as easily as with amber topology.
Thanks,
Song-Ho
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Received on Thu Mar 10 2016 - 05:00:03 PST
