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Can yank be used to calculate the binding energy of proteins and peptides?

2

Question as the title, can yank be used to calculate the binding energy of proteins and peptides?

dxli75

yank found unknown parameter number_of_iterations in all examples. I changed nothing, just running

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(base) root@bash#t4-lysozyme$ yank script --yaml=p-xylene-implicit.yaml found unknown parameter number_of_iterations Traceback (most recent call last): File "/userhome/dxli-data/program/anaconda3/lib/python3.7/site-packages/yank/experiment.py", line 1191, in _validate_options special_conversions=special_conversions) File "/userhome/dxli-data/program/anaconda3/lib/python3.7/site-packages/yank/utils.py", line 1058, in validate_parameters raise TypeError("found unknown...

dxli75

Hi, I am running a binding free energy calculation by means of YANK and encountered the following. Starting from a well equilibrated amorphous polymer structure I initiate the YANK simulation....

Eli-VDB

REMD Performance

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I am working on REMD . I set up the simulation using the worked out example proposed in link : [REMD Openmmtools](https://openmmtools.readthedocs.io/en/0.18.1/api/generated/openmmtools.multistate.ReplicaExchangeSampler.html) I installed openmm,openmmtools and yank using conda .I...

shitanshu-cell

Incorporate QM into ligand parameterization pipeline

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As a YANK newbie, it seems the existing ligand parameterization pipeline doesn't use any ab initio QM calculations. Since Schrodinger runs their force field builder and Jaguar to fill in...

tantrev

Parallel simulation using slurm queue

3

Let us assume that there are three nodes and each node has 8-GPUs. Is it possible to leverage 24 GPUs simultaneously if there are more than 24 lambda points? In...

jslim-furame

Error with reading yaml file

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Hi yank users, I've been trying to calculate absolute binding free energy with YANK. But I encountered the error as below: ``` yaml.scanner.ScannerError: mapping values are not allowed here in...

Byun-jinyoung

Using yank for calculation of mixing free energy

3

hello, I would like to use the YANK program to calculate mixing free energies for a polymer-drug system. I figured that the mixing free energy could be calculated in similar...

Eli-VDB

Now revealed by the GH Actions pipeline.

jaimergp

Setting problem during absolute binding energy calculation (maybe in complex phase...?)

2

When I run the absolute calculation protocol, I got the error below ``` /home/juyong/apps/amber18/bin:/home/juyong/anaconda3/envs/yank/bin:/usr/local/cuda-10.1/bin:/appl/anaconda3/envs/openmm_env/bin:/appl/mpi/intel/openmpi-4.0.2/bin:/usr/local/cuda-10.1/bin/:/opt/intel/advisor_2017.1.5.527008/bin64:/opt/intel/vtune_amplifier_xe_2017.6.0.554757/bin64:/opt/intel/inspector_2017.1.4.527006/bin64:/opt/intel/itac/2019.5.041/intel64/bin:/opt/intel//itac/2019.5.041/intel64/bin:/opt/intel//clck/2019.5/bin/intel64:/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/opt/intel/debugger_2019/gdb/intel64_mic/bin:/opt/gromacs-2019.4-plumed/bin:/home/byun/anaconda3/bin:/home/byun/anaconda3/condabin:/home/juyong/apps/amber18/bin:/opt/mmpbsa/bin:/opt/APBS-1.4/bin:/opt/plumed-2.5.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home/juyong/apps/amber18/bin:/home/choi/docking/ucsf/dock6/bin:/home/byun/apps/GalaxyDock3/bin:/home/byun/.local/bin:/home/byun/bin:/opt/intel/parallel_studio_xe_2017.8.066/bin /home/juyong/anaconda3/envs/yank/bin/mpirun 2020-10-12 16:54:25,297: Setting CUDA platform to use precision model 'double'. 2020-10-12 16:54:25,396: WARNING - openmmtools.multistate.multistatesampler...

Byun-jinyoung