luancarvalhomartins PyAutoFEP issues

luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

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issues

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

#144 Ranjita-ACOG opened 2 months ago
0
Error while run analyze_results.py : IndexError: list index out of range

#143 lihuishanghaitech opened 3 months ago
2
Runing examples Generate Perturbation Map erros: ValueError: Molecule not found

#142 ninomiya829 closed 3 months ago
0
ModuleNotFoundError: No module named 'merge_topologies'

#140 Teng-Dan opened 4 months ago
0
prepare_dual_topology.py --config_file=step2.ini issues

#139 wenzeyu126553 opened 6 months ago
1
Error in prepare_dual_topology.py while working on perturbation pose coordinates

#138 dpetrov835 opened 6 months ago
0
Query regarding prepare_dual_topology.py

#137 saikat0003 opened 6 months ago
0
Can anyone serve a former code?

#136 Jiang-Lu-CAS opened 6 months ago
0
Tutorial error in the "water/nvt" process (nvt_grompp.log: Fatal error: Invalid atom number 3780 in indexfile)

#135 Jiang-Lu-CAS opened 7 months ago
2
Can we assess that FEP has converged based on this graph?

#134 1200Caixia opened 7 months ago
1
Error in prepare_dual_topology.py

#133 Arikite-netizen opened 7 months ago
0
UnicodeDecodeErrorv when running prepare_dual_topology

#132 xrik closed 9 months ago
1
Invalid atom number 3804 in indexfile

#131 whe280 opened 9 months ago
10
Error in command 'prepare_dual_topology.py'

#129 gsaha322 opened 10 months ago
1
how to add other ligands that do not require FEP calculations?

#128 aw10279 opened 10 months ago
1
Absolute rather than relative path in scripts

#127 Moricant opened 11 months ago
1
Solvation Error

#126 mudit-git opened 11 months ago
5
Unable to run script prepare_dual_topology.py

#125 kong0706 opened 11 months ago
1
Computer rebooted after prepare_dual_topology.py

#124 kolmorgan opened 11 months ago
0
errors about prepare_dual_topology.py

#123 zh2417 opened 1 year ago
3
some questions about results

#121 zh2417 closed 1 year ago
1
analyzing error using tutorial.tgz

#120 Samuel-gwb opened 1 year ago
3
mpirun mdrun fails with`There are not enough slots available`

#119 zh2417 closed 1 year ago
1
Analyzing incomplete runs

#118 xy21hb opened 1 year ago
4
error about gmx

#117 zh2417 closed 1 year ago
1
Problems with using Cgenff topologies

#116 pallavsen007 closed 1 year ago
3
Unable to generate dual topology files

#115 pallavsen007 opened 1 year ago
9
Resolution of XTC Generation Issue in run.sh with 'echo' Command Enhancement

#114 AzraelXu closed 8 months ago
8
add_ligand_to_solvated_receptor() got an unexpected keyword argument 'index_data' when pre_solvated=True

#113 AzraelXu closed 1 year ago
26
Error in running runall.sh with GROMACS2021

#112 camputchem opened 1 year ago
11
rename_res.sh not found

#111 futianfan closed 1 year ago
2
`analyze_results.py` Segmentation fault

#110 xy21hb opened 1 year ago
1
Mismatch Results

#108 xy21hb closed 1 year ago
1
MD crashes

#107 VesperChen01 closed 1 year ago
5
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 xy21hb closed 1 year ago
2
auto prepare top example

#105 xy21hb opened 1 year ago
7
Parallelize equilibration using `gmx mdrun -multidir`

#104 luancarvalhomartins opened 1 year ago
0
`analyze_results.py`: Could not find a path to connect nodes AAA and BBB. Cannot go on.

#102 Liaokang123456 closed 1 year ago
4
water leg broken

#101 xy21hb closed 1 year ago
6
How to use pyautofep calculation when the ligand is peptide

#100 CPU-HORDB closed 1 year ago
1
Failed to run gmx make_ndx. Error code 11

#99 camputchem opened 1 year ago
2
mpirun vs nve dilemma

#98 xy21hb closed 1 year ago
1
"There is no domain decomposition for XX ranks" when running nve equilibration.

#97 xy21hb closed 1 year ago
4
Generate Perturbation Map Hanging

#96 hongsrich opened 1 year ago
6
Using system loader (ie, a pre-solvated system) and pdb2gmx -ignh parameter

#95 Tiamo6174 closed 1 year ago
6
The FEP calculation results are very different when rest2 is started and when rest2 is not started.

#94 1200Caixia closed 1 year ago
2
Core dumped when running the nve of runall.sh

#93 Layne-Huang opened 1 year ago
7
Tutorial fails at tutorial/FXR_12-FXR_74/protein/lambda1/min01

#92 JecaTosovic closed 1 year ago
1
tutorial FXR PDB numbering problem

#91 xy21hb opened 1 year ago
1
Can't run analyze_results.py

#90 hlzfoxcn closed 1 year ago
4