Add support for gaff2

[xiki-tempula]

Fix #10 Add support for gaff2.

Note that the HW and OW which is the oxygen and hydrogen in the TIP3P water are not formally defined in the gaff2 file and thus, their epsilon and sigma are set to zero. This should not matter to small molecule parameterization unless someone wants to parameterise water.

[selimsami]

Also, there are few more places you need to change:

• adding gaff2 to the list of LJs
• Change this line to something like: elif config.lennard_jones.startswith('gaff')

[xiki-tempula]

@selimsami Thanks for the review and I have made changes to the files.
With regard to gaff2.py, I do agree that it is not necessary for the qforce. However, given that the gaff2.dat is not officially provided by the amber, I think it might be a good idea to put it there such that people could see how this file is being generated (e.g. how is the unit being converted).

[selimsami]

@selimsami Thanks for the review and I have made changes to the files. With regard to gaff2.py, I do agree that it is not necessary for the qforce. However, given that the gaff2.dat is not officially provided by the amber, I think it might be a good idea to put it there such that people could see how this file is being generated (e.g. how is the unit being converted).

maybe it would be better to start the 'gaff2.dat' (this better be gaff2.itp) with a comment on how this file was generated (parmed + unit conversion). I really think it's not necessary to have this file in qforce rep.

[xiki-tempula]

@selimsami Thanks for the review, I have renamed gaff2.dat and removed the gaff2.py.

[selimsami]

Fix #10 Add support for gaff2.

I do not understand the purpose of the gaff2.py file. Is that necessary?

Note that the HW and OW which is the oxygen and hydrogen in the TIP3P water are not formally defined in the gaff2 file and thus, their epsilon and sigma are set to zero. This should not matter to small molecule parameterization unless someone wants to parameterise water.

Parametrizing water with qforce is not a great idea... :-D so I think it's fine.