Run Katachi Amendment

After parameterization, run:

katachi.py ihf_result_mmH2O2.com 0 calcall 100

The result will be named katachi_ihf_result_mmH2O2.com.

Here are the last lines of the example:

AmbTrs   ho  oh  oh  ho   0   0   0   0    0.000  1.552  0.000  0.000   1.0
HrmBnd1 ho oh oh   68.779  98.2714
HrmStr1 ho oh   550.931  0.96915
HrmStr1 oh oh   346.974  1.44835
Nonbon 3 1 0 0 0.0 0.0 0.5 0.0 0.0 -1.2
VDW    ho  0.0000  0.0000
VDW    oh  1.7210  0.210

The detailed usage is as follows.

> katachi.py --help
usage: katachi.py [-h] mmresult loopid opt convthreshold
positional arguments:
  mmresult       parameterized result MM file.
  loopid         loopid
  opt            opt or calcall
  convthreshold  convergence threshold

loopid is the number of starting cycle. It should be 0 if it is a fresh run. If Katachi was interrupted in the middle, this number can be set to that of the latest cycle to restore the process.

opt or calcall controls the commands used for MM optimization. If opt is specified, opt=(nomicro,cartesian) will be used for MM optimization, and after the convergence, opt=(nomicro,cartesian,tight,calcall) will then be used and start again from the previous result. If calcall is specified, all steps will use the latter keywords. In practice, we found that using calcall is usually better.

convthreshold is the cycle number threshold. If the result does not improve any more in the given cycles, the program will stop. In our tests, we used 100 for this threshold; that means, if the result does not improve in 100 cycles, the program will stop and use the best result before.