[FEATURE] Support for glycam and ff12

[jmichel80]

We do occasionally work with glycoproteins is there a way to add this support so we can load these systems into BSS? I think using tleap and pdb4amber in BSS should be out of scope but reading in topologies with sugars but I think we would like to be able to read in topologies with sugars. We have already hit this as an issue.

I guess it shouldn’t be the biggest problem just that when you use sugars you normally have to use ff12SB. So I guess we may need an override flag or something.

[lohedges]

From my reading of the AmberTools manual, it looks like GLYCAM is supported for ff14SB by adding:

source leaprc.GLYCAM_06j-1

(It only mentions ff14SB but perhaps it works with older versions of the forcefield too. The GLYCAM website is horribly out of date, but mentions ff99SB onwards.)

From reading the tLEaP output, this also pulls in tip3p ion parameters for monovalent ions, so perhaps we also need to be careful combining this with our ion handling.

Currently trying to find some example glycoproteins that work. A quick search of the PDB hasn't provided anything useful, yet.

[lohedges]

While I've not yet come up with a specific implementation, this could probably be solved using the same approach as this, i.e. the use could load the required parameters using the optional leap_commands parameter.