xy21hb

tutorial.tgz request

1

Anyone has tutorial.tgz in the Tutorial, I have spent quite some time but still could not proceed to the Analysis step. I would be so grateful if someone could share...

Analyzing incomplete runs

4

If some pairs are broken, could analyze_results.py still work, suppose e.g. if only FXR_12_FXR_88 pair of the tutorial is broken, e.g. system is unstable, only intermediate pdbs are written and...

auto prepare top example

7

Any example on how to use prepare_dual_topology.py to generate gmx top file for ligands? The manual says it uses AcPYPE, but if I have a list of ligands, can I...

`analyze_results.py` Segmentation fault

1

analyze_results.py --input tutorial1.tgz --units kcal --output_uncompress_directory tutorial_results --center_molecule=FXR_12 /share1-100G/dump/PyAutoFEP-master/docs/tutorial01/tutorial1/../../../analyze_results.py:1365: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if version_fn(alchemlyb_version) != version_fn('0.3.0') and version_fn(alchemlyb_version) < version_fn('0.6.0'): All available analysis will...

tutorial FXR PDB numbering problem

1

 ============ Dear all, I am trying to run the current version tutorial FXR, and I guess the prepared PDB has some problems with numbering, anyone has met this problem...

ATOM 1 O7N NAD B 1 -18.523 -4.437 19.312 1.00 20.63 O ATOM 2 C7N NAD B 1 -17.694 -4.517 20.210 1.00 18.83 C ATOM 3 N7N NAD B 1...