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.