Fix parmconv

[chrisbarnettster]

Hi everyone

These changes should fix the issue as mentioned on the Gitter chat. I also updated versions for the AmberTools (part of refactoring tool versioning that was started by @bgruening and @simonbray)

@bgruening is it possible to test this on the .gro .top that were causing issues?

Bigger changes:

• Allowing saving of .mdout when keep files set to yes. This will help with debugging as user can access a collection of .mdout files
• Adding functionality to allow MMPBSA runs to work properly. Allow removal of dihedrals with no periodicity and allow removal of box periodicity info
  • When using MMPBSA there are sometimes issues with dihedrals that have no periodicity (i.e. constant energy term) that doesn't seem to be supported - see http://archive.ambermd.org/201912/0082.html. These are to be removed
  • The models used in MMPBSA tend not to support periodic cells. Traj's should be imaged/wrapped as need be then compared. Building an option to remove cell information.

[bgruening]

@bgruening is it possible to test this on the .gro .top that were causing issues?

Oh the user-issue that I was reporting ...? I think @tsenapathi has a shared history. This could be tested locally in planemo?

[bgruening]

Thanks a lot for fixing it!

[chrisbarnettster]

@bgruening is it possible to test this on the .gro .top that were causing issues?

Oh the user-issue that I was reporting ...? I think @tsenapathi has a shared history. This could be tested locally in planemo?

yes I will do this now

[chrisbarnettster]

@simonbray is this working for your usecase?

[simonbray]

@simonbray is this working for your usecase?

Yes, I am not doing anything fancy, but I needed the remove box and dihedral options.

[simonbray]

@chrisbarnettster do you want to finish this or shall I continue? I'll have some time later on.

Either is fine, just want to make sure we are not dupiicating work.

[chrisbarnettster]

Hi @simonbray, I just updated a version for MMPBSA as I noted that there was minor change. Is there anything else worth doing here? Yes I am happy for you to go ahead and finalise. Let me know if you need anything :)

[simonbray]

Okay will do. :)

[chrisbarnettster]

ready for review? @simonbray

[simonbray]

ready for review? @simonbray

Yes, I think so. :+1:

[chrisbarnettster]

Hi @simonbray I did a check of tests and had another look at the code. Seems good to merge. Have also checked by using the T4 Lysozyme system, and the process from using parmconv to calculating MMGBSA energies works. Seems that you and @bgruening are the official reviewers as I submitted the original PR. Anything else needed?

[simonbray]

No looks good, thanks @chrisbarnettster