Absolute Binding Free Energy Calculations with GROMACS about biosimspace HOT 7 CLOSED

Hi there.

Have you tried running this using the Exscientia fork? There have been a few one-way synchronisations (from us to them) recently, which have passed all of their internal checks, but there haven't been any synchronisations the other way. I've not written (or tested) any of this part of the codebase, so I'm not the best placed to answer.

However, the mdp files generated contained the line couple-moltype = , which should have been couple-moltype = LIG. mol._sire_object.name().value() was returning an empty string here.

This part of the code is identical in their fork, so presumably the same issue would occur. (Unless the name is being returning an empty string due to some Sire API changes?)

Tagging @xiki-tempula. Feel free to move this issue over to your fork if needed.

from biosimspace.

Thanks for the reply. I've just tried with the Exscientia fork and I still get the empty couple-moltype issue.

from biosimspace.

If you save the lig = BSS.Align.decouple(system[0]) into a gromacs topology, does it has a name?

from biosimspace.

Yes, its name is LIG, as with the input generated above. The end of the topology file shows

[ molecules ]
;molecule name    nr.
           LIG      1

Thanks.

from biosimspace.

@fjclark Can you load this topology file back in. Replacing the line system = BSS.IO.readMolecules(["input/SYSTEM.top", "input/SYSTEM.crd"])
and do everything again to see if it works?

from biosimspace.

@xiki-tempula that solves the issue. Now couple-moltype = LIG, and the gradients with respect to coul-lambdas and vdw-lambdas are non-zero. Thanks very much!

from biosimspace.

Thanks for solving. I'd suggest adding some fallback in case the input was generated via another means, since not all of the parsers apply a molecule name in this way, e.g. I'm not sure if it would always be persistent on save/load depending on the format.

from biosimspace.