Yanze Wang

New features that need TensorFlow link want to contribute

7

Hi all, We(@amcadmus, @njzjz, @TablewareBox, @Dead-fisher) want to contribute our new features to PLUMED2, which can read TensorFlow graph files and use their outputs as biased force adding to the...

Hi, It's not a real issue, but I would like to explore more about the comparison between the two provided samplers in `openmmtools`, SAMS & REMD. Practically, I can run...

AmberPrmtopFile.__init__() got an unexpected keyword argument 'periodicBoxVectors'

2

Hi, I am starting simulations from amber formatted files by: ``` inpcrd = app.AmberInpcrdFile(inpcrd_file) prmtop = app.AmberPrmtopFile(prmtop_file, periodicBoxVectors=inpcrd.boxVectors) system = prmtop.createSystem(nonbondedMethod=app.PME, nonbondedCutoff=1.0*unit.nanometers, constraints=app.HBonds) ``` This is suggested in the tutorial,...

[Questions] How to handle `top` with `amber14ff`

5

Hi, I am using `PyAutoFEP` to calculate the free energy values of 3 pairs. Previously, my other simulations were conducted by `amber14ff` via `gromacs-2022` and I would like to use...

Could ligand preparation be accelerated, e.g. using multiprocessing, when drug library is huge?

1

Hi, I'm using `Unidock` command line. I just found when the molecule library is in a huge number, the time for ligand preparation is too long and GPUs has nothing...

Can't find mgltools properly

1

Hi, Based on code here: https://github.com/dptech-corp/Uni-Dock/blob/7c0cda06c94fc802194c55e7cec0cef1f834c31a/unidock_tools/unidock_tools/protein_prepare/protein_prepare.py#L14-L32 I thought this way to find mgltools is not good. I was assuming users are under `Unidock tools` conda env where Unidock are installed...

Error: could not open "" for reading.

3

Scripts: ```bash Unidock --receptor 1ipb_protein_only.pdbqt \ --ligand_index ligands.idx \ --reference ligands/M7G.sdf \ --scoring vina \ --center_x 10.671 \ --center_y -73 \ --center_z 22. \ --size_x 20 \ --size_y 20 \...