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How to configure yank script when the receptor includes coenzyme

4

Dear all, Recently I found that yank could not calculate free energy when the pdb of the receptor contains coenzyme such as FAD (PDB ID: 4kw5), but this fad interacts...

kingljy0818

Use Open Force Field parameters for ligands

20

There is no clear way to use Open Force Field parameters for ligands, as the YAML input takes in mol2 and leaprc.gaff. Maybe if the ligands could be set up...

daveminh

If you want to incorporate a binding pose prediction into YANK, this code that I wrote today could be a helpful reference. This extracts the bound state and aligns it:...

daveminh

Dear all, For the alchemical_path of complex and solvent of protocol parameter in * .yaml, I have some questions. Could the alchemical_path of complex and solvent be both set to...

kingljy0818

How to enable the parallel mode in two gpus server

4

Dear all, I have a two GPUS (1080Ti) server includes two CPUs, when I perform the test command: build_mpirun_configfile "yank script --yaml=p-xylene-implicit.yaml" I will get the error: build_mpirun_configfile "yank script...

kingljy0818

mpi4py should be a dependency of conda installer

3

I got this error from a fresh install from miniconda3 when running on XSEDE Bridges. Traceback (most recent call last): File "/home/dminh/.conda/envs/yank/bin/yank", line 11, in load_entry_point('yank==0.25.2', 'console_scripts', 'yank')() File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/cli.py",...

daveminh

Implementing RMSD or other restraints in solvent phase

2

Currently, the yank documentation says: "The RMSD restraints must also be applied in the solvent phase of the calculation if they are on in the decoupled state, but this is...

jeffcomer

This looks useful: https://github.com/duecredit/duecredit

jchodera

During minimization, Yank continues using 100% of the CPU, but doesn't write any output or log entries. For example, I replaced "type: Harmonic" with "type: RMSD" in the example "p-xylene-explicit.yaml"....

jeffcomer

run yank on specific gpu?

10

Hi , i would like run multiple yank at the same time for different protein/ligand each on different gpu. i have 6 gtx 1080 on my machine but i dont...

sawstory