tleap ToDo

[nhenriksen]

• if pbc_type is None there is very little filtering of template lines. We probably need to at least get rid of quit lines. Also, if output_prefix is not None we should probably get rid of saveamberparm in template_lines
• Write tleap output to a log file in each window. We also need to figure out what to do for organized logging overall, but I think this should definitely go in each window subdir ... for reference purposes.

[slochower]

Okay. Should we have the ability to write a default salvation input file, if there is no template and no template list of strings? In other words, should we expect everyone who uses paprika know how to use tleap?

[nhenriksen]

Seems like a good idea, but how would it work? You have to have a force field (leaprc) plus solute frcmods and mol2s at minimum. Those are always different. I think we have to expect that anyone who uses paprika.tleap will know how to use tleap.