Selection of Nter, Cter and 5'end states at topology generation

[VGPReys]

You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines.

Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

This PR adds three new parameters in the topoaa module enabling the tune the states of Nter and Cter residues.
These parameters are molecule parameters (topoaa.molX), and can be specified for all molecules.

• charged_nter: This option defines how N-terminus residue should be. If false (default), N-ter will be an uncharged NH as it would be in a peptide bond. If true, N-ter will be a charged NH3+. (default false)
• charged_cter: This option defines how N-terminus residue should be. If false (default), C-ter will be an uncharged CO, as it would be in a peptide bond. If true, C-ter will be a charged COO-. (default false)
• 5_phosphate: This parameter defines how 5' ends on nucleic acids should be. If false (default), 5' end will be an OH. If true, 5' end will be a phosphate.

Related Issue

Closes #1269

Haddock3 user manual PR 13

Additional Info

Todo:

• add integration tests
• make sure it is functional when self_contained = true
• update user manual
• Add DNA 5' termini selection

[amjjbonvin]

Just some cleaning of the CNS script - see comment - then can be approved

[amjjbonvin]

I am making some more cleaning, removing the unnecessary file. Everything is this pull request at this time is fine.
I will soon push additional changes.

[VGPReys]

We will need someone else to review this branch before merge as we are both authors

[AnnaKravchenko]

It would be nice to indicate in the log file that "custom termini state has been applied”
Or even more detailed: "Molecule 1: charged termini” “Molecule 2: uncharged termini”

[AnnaKravchenko]

For charged N-ter I expect to see 3 atoms of H, but I see 3 atoms of HT:

ATOM      8  HT1 MET A   1      14.442   3.700 -14.277  1.00 15.00      A    H
ATOM      9  HT2 MET A   1      15.085   4.703 -13.075  1.00 15.00      A    H
ATOM     10  HT3 MET A   1      14.374   5.378 -14.451  1.00 15.00      A    H

Apparently it’s normal, but I would add a note to user manual saying that terminal hydrogens are not ‘H’ but ’TH’.
But also maybe it’s my lack of knowledge, and so not relevant. Someone else should make final call

[AnnaKravchenko]

Note to slef/to user-guide/to add comment in code/etc:
Often dsDNA is given to Haddock as a sidngle chain with ‘TER’, e.g. res 1-11; TER; res 12-22
In this case, 5_phosphate=true will add atoms only to the res1, and not to res12. And this is fine, becuase res12 already has almost comptele phosphate except for 1 Hydrogen.

[VGPReys]

For charged N-ter I expect to see 3 atoms of H, but I see 3 atoms of HT:

ATOM      8  HT1 MET A   1      14.442   3.700 -14.277  1.00 15.00      A    H
ATOM      9  HT2 MET A   1      15.085   4.703 -13.075  1.00 15.00      A    H
ATOM     10  HT3 MET A   1      14.374   5.378 -14.451  1.00 15.00      A    H

Apparently it’s normal, but I would add a note to user manual saying that terminal hydrogens are not ‘H’ but ’TH’. But also maybe it’s my lack of knowledge, and so not relevant. Someone else should make final call

This is standard nomenclature, same of the OXT

[VGPReys]

Note to slef/to user-guide/to add comment in code/etc: Often dsDNA is given to Haddock as a sidngle chain with ‘TER’, e.g. res 1-11; TER; res 12-22 In this case, 5_phosphate=true will add atoms only to the res1, and not to res12. And this is fine, becuase res12 already has almost comptele phosphate except for 1 Hydrogen.

Ok, I wil add in the manual that chain breaks are not evaluated as termini

[AnnaKravchenko]

Tested for proteins, dsDNA and ssRNA - all is functional!

I did not spend enough time investigating how this change influences calculation of rmsd, but at a glance everything is fine