Noah

Hi Esther, Having given it some more thought it sounds like it's more work than it's worth! I think having used this package a fair bit I can now just...

I actually just decided to implement a relatively naive version of this myself. The code only works when supplying PDB files as input: Checks for align_cofactors arg, if True then...

Hi Lester, Thanks for getting back to me and checking this. Reassuring that [atoms] directive takes precedence over [atomtypes] and this shouldn't make a difference to FEP calcs. Just to...

> I would suggest a gentle equilibration protocol that raises temperature gradually with restraints on ligand and protein atoms to begin with, followed by gradual release. The following node may...

Hi @annamherz >I have also been having instability issues for this type of perturbation as well, and it is able to proceed at a lower timestep with no HMR. I'm...

Okay good news - switching from HMR scaling factor of 4 to 3 prevents the solvent leg of the simulation breaking, while retaining the 4fs timestep! Feeling optimistic that this...

>Hello! Doing this also meant my solvent leg was no longer failing, however my bound leg is still failing for the CH3 -> CH2-cyclopropyl with a factor of 3. I...

Thanks for the info both of you. I have had some success with unrestrained but RMS fitted trajectories using AmberTools22. I don't know whether the PME version is included in...

Are there any other options for providing input to grand, rather than PDBFile (with conect records) + ligand XML? I've been trying to use .gro and .top input files but...

Oops sorry was working with two molecules then cut one out when I wrote this post. Have edited the original post