luancarvalhomartins/PyAutoFEP

Issues

• Absolute rather than relative path in scripts

  #127 opened a year ago by Moricant
  1

• Invalid atom number 3804 in indexfile

  #131 opened a year ago by whe280
  10

• Not printing any dVcoul/dl or dVvdw/dl in the md.log file

  #144 opened 6 months ago by Ranjita-ACOG
  0

• Resolution of XTC Generation Issue in run.sh with 'echo' Command Enhancement

  #114 opened a year ago by AzraelXu
  8

• Can we assess that FEP has converged based on this graph?

  #134 opened a year ago by 1200Caixia
  1

• Error while run analyze_results.py : IndexError: list index out of range

  #143 opened 7 months ago by lihuishanghaitech
  2

• Runing examples Generate Perturbation Map erros: ValueError: Molecule not found

  #142 opened 7 months ago by ninomiya829
  0

• Solvation Error

  #126 opened a year ago by mudit-git
  5

• ModuleNotFoundError: No module named 'merge_topologies'

  #140 opened 8 months ago by Teng-Dan
  0

• UnicodeDecodeErrorv when running prepare_dual_topology

  #132 opened a year ago by xrik
  1

• prepare_dual_topology.py --config_file=step2.ini issues

  #139 opened 9 months ago by wenzeyu126553
  1

• Error in prepare_dual_topology.py while working on perturbation pose coordinates

  #138 opened 9 months ago by dpetrov835
  0

• Query regarding prepare_dual_topology.py

  #137 opened 10 months ago by saikat0003
  0

• Can anyone serve a former code?

  #136 opened 10 months ago by Jiang-Lu-CAS
  0

• Tutorial error in the "water/nvt" process (nvt_grompp.log: Fatal error: Invalid atom number 3780 in indexfile)

  #135 opened 10 months ago by Jiang-Lu-CAS
  2

• Error in running runall.sh with GROMACS2021

  #112 opened a year ago by camputchem
  11

• Error in prepare_dual_topology.py

  #133 opened a year ago by Arikite-netizen
  0

• Error in command 'prepare_dual_topology.py'

  #129 opened a year ago by gsaha322
  1

• how to add other ligands that do not require FEP calculations?

  #128 opened a year ago by aw10279
  1

• Unable to run script prepare_dual_topology.py

  #125 opened a year ago by kong0706
  1

• Computer rebooted after prepare_dual_topology.py

  #124 opened a year ago by kolmorgan
  0

• errors about prepare_dual_topology.py

  #123 opened a year ago by zh2417
  3

• analyzing error using tutorial.tgz

  #120 opened a year ago by Samuel-gwb
  3

• add_ligand_to_solvated_receptor() got an unexpected keyword argument 'index_data' when pre_solvated=True

  #113 opened a year ago by AzraelXu
  26

• mpirun mdrun fails with`There are not enough slots available`

  #119 opened a year ago by zh2417
  1

• some questions about results

  #121 opened a year ago by zh2417
  1

• Analyzing incomplete runs

  #118 opened a year ago by xy21hb
  4

• Problems with using Cgenff topologies

  #116 opened a year ago by pallavsen007
  3

• Unable to generate dual topology files

  #115 opened a year ago by pallavsen007
  9

• error about gmx

  #117 opened a year ago by zh2417
  1

• auto prepare top example

  #105 opened a year ago by xy21hb
  7

• MD crashes

  #107 opened a year ago by VesperChen01
  5

• rename_res.sh not found

  #111 opened a year ago by futianfan
  2

• `analyze_results.py` Segmentation fault

  #110 opened a year ago by xy21hb
  1

• water leg broken

  #101 opened a year ago by xy21hb
  6

• Using system loader (ie, a pre-solvated system) and pdb2gmx -ignh parameter

  #95 opened a year ago by Tiamo6174
  6

• Mismatch Results

  #108 opened a year ago by xy21hb
  1

• analyze_results.py:578: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. processed_u_nk = processed_u_nk.append(each_structure_block)

  #106 opened a year ago by xy21hb
  2

• `analyze_results.py`: Could not find a path to connect nodes AAA and BBB. Cannot go on.

  #102 opened a year ago by Liaokang123456
  4

• Parallelize equilibration using `gmx mdrun -multidir`

  #104 opened a year ago by luancarvalhomartins
  0

• "There is no domain decomposition for XX ranks" when running nve equilibration.

  #97 opened a year ago by xy21hb
  4

• How to use pyautofep calculation when the ligand is peptide

  #100 opened a year ago by CPU-HORDB
  1

• Failed to run gmx make_ndx. Error code 11

  #99 opened a year ago by camputchem
  2

• mpirun vs nve dilemma

  #98 opened a year ago by xy21hb
  1

• Generate Perturbation Map Hanging

  #96 opened 2 years ago by hongsrich
  6

• The FEP calculation results are very different when rest2 is started and when rest2 is not started.

  #94 opened 2 years ago by 1200Caixia
  2

• Core dumped when running the nve of runall.sh

  #93 opened 2 years ago by Layne-Huang
  7

• Can't run analyze_results.py

  #90 opened 2 years ago by hlzfoxcn
  4

• Tutorial fails at tutorial/FXR_12-FXR_74/protein/lambda1/min01

  #92 opened 2 years ago by JecaTosovic
  1

• tutorial FXR PDB numbering problem

  #91 opened 2 years ago by xy21hb
  1