I need to optimize a force field I generated. For this, I should apply Genetic Algorithm (G.A). To apply G.A I should do this for 220 molecules:

1) Find all dihedrals for each molecule ( I did this already with parmchk)

2) Rotate all dihedrals (10-20 degree step in 90 or 360 degree range) and save a mol2 file at each steps.

3) Change all angles (1-2 degree step in 20 or 30 degree range)and save a mol2 file at each step.

Now, I need a program to do this because 220 molecules are too much. I tried "tleap" but it was unstable. I tried pymol but I couldn't run command directly via "cmd" or "terminal" (if there is a way I don't know). So which program should I use?

  • $\begingroup$ Have you tried to automate these with ase (wiki.fysik.dtu.dk/ase/index.html)? $\endgroup$ – Greg May 6 at 17:18
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    $\begingroup$ I think it would be beneficial, if you were to tell us which operating system you are restricted to (or none of that applied). $\endgroup$ – Martin - マーチン May 6 at 18:28
  • $\begingroup$ If you know Python you can modify this program github.com/jensengroup/get_conformations $\endgroup$ – Jan Jensen May 7 at 6:58
  • $\begingroup$ Martin, I am using vbox so os doesn't make any difference. I am using win10pro + ubuntu bash in windows and kali linux and ubuntu and opensuse in my vbox. $\endgroup$ – Baris Vvolf May 12 at 17:05
  • $\begingroup$ Greg and jan jensen, i will try your advices. Thank you by now. $\endgroup$ – Baris Vvolf May 12 at 17:06

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