prepare_dual_topology.py --config_file=step2.ini

[hexuhua69]

$ prepare_dual_topology.py --config_file=step2.ini
=============== mdp and run steps=================
Complex Water
min01.mdp min01.mdp
min02.mdp min02.mdp
min03.mdp nve.mdp
nve.mdp nvt.mdp
nvt.mdp npt.mdp
npt.mdp md.mdp
md.mdp -

================= Input ligands ==================
Name Molecule Topology
FXR_12 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(Cl)c1[H] lig_data/FXR_12.itp
FXR_74 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(Br)c1[H] lig_data/FXR_74.itp
FXR_76 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c([H])c1[H] lig_data/FXR_76.itp
FXR_84 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(F)c1[H] lig_data/FXR_84.itp
FXR_85 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(C([H])([H])[H])c1[H] lig_data/FXR_85.itp
FXR_88 [H]c1c([H])c([H])c(S(=O)(=O)N2C([H])([H])C([H])([H])C3(C(=O)N(C([H])([H])c4c([H])c([H])c(C(=O)[O-])c([H])c4[H])c4c([H])c([H])c(Br)c([H])c43)C([H])([H])C2([H])[H])c(C(F)(F)F)c1[H] lig_data/FXR_88.itp

================= Perturbations ==================
State A State B
FXR_12 FXR_74
FXR_12 FXR_76
FXR_12 FXR_84
FXR_12 FXR_85
FXR_12 FXR_88

=================== Poses read ===================
Name File Details
FXR_12 {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x14d8a677f6b0>, 'topology': ['lig_data/FXR_12.itp']}
=============== Superimposed poses ===============
Name File Note
FXR_12 {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x14d8a677f6b0>, 'topology': ['lig_data/FXR_12.itp']} Read from saved state

================== Align poses ===================
Molecule FXR_12 aligned
================ Working on pairs ================
Perturbation Pose Coordinates
============ Working on FXR_12-FXR_74 ============
FXR_12→FXR_74
================ Building system =================

=================== STACK INFO ===================
File "/mnt/e/software/gromacs-2021/build/PyAutoFEP/prepare_dual_topology.py", line 4575, in
verbosity=arguments.verbose
File "/mnt/e/software/gromacs-2021/build/PyAutoFEP/os_util.py", line 558, in wrap_trace
return f(*args, **kwargs)
File "/mnt/e/software/gromacs-2021/build/PyAutoFEP/prepare_dual_topology.py", line 742, in prepare_complex_system
msg_verbosity=os_util.verbosity_level.error, current_verbosity=verbosity)
File "/mnt/e/software/gromacs-2021/build/PyAutoFEP/os_util.py", line 313, in local_print
formatted_string = '\n{:=^50}\n{}{:=^50}\n'.format(' STACK INFO ', ''.join(traceback.format_stack()),
=================== STACK INFO ===================
[ERROR] Failed to run gmx grompp. Error code 1.
[ERROR] Command line was: ['gmx', 'grompp', '-f', '/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/genion_step5_094106_01112024.mdp', '-c', '/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolvated_step4_094106_01112024.gro', '-p', '/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolv_step4_094106_01112024.top', '-o', '/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/genion_step6_094106_01112024.tpr', '-maxwarn', '1', '-po', '/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/mdout_step6_094106_01112024.mdp']
[ERROR]
[ERROR] stdout:
[ERROR] Setting the LD random seed to -303170244
[ERROR]
[ERROR] Generated 449826 of the 449826 non-bonded parameter combinations
[ERROR]
[ERROR] Generated 449826 of the 449826 1-4 parameter combinations
[ERROR]
[ERROR] Excluding 3 bonded neighbours molecule type 'Protein'
[ERROR]
[ERROR] Excluding 3 bonded neighbours molecule type 'Protein2'
[ERROR]
[ERROR] Excluding 3 bonded neighbours molecule type 'LIG'
[ERROR]
[ERROR]
[ERROR] stderr:
[ERROR] :-) GROMACS - gmx grompp, 2021 (-:
[ERROR]
[ERROR] GROMACS is written by:
[ERROR] Andrey Alekseenko Emile Apol Rossen Apostolov
[ERROR] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[ERROR] Christian Blau Viacheslav Bolnykh Kevin Boyd
[ERROR] Aldert van Buuren Rudi van Drunen Anton Feenstra
[ERROR] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[ERROR] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[ERROR] Aleksei Iupinov Christoph Junghans Joe Jordan
[ERROR] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[ERROR] Carsten Kutzner Per Larsson Justin A. Lemkul
[ERROR] Viveca Lindahl Magnus Lundborg Erik Marklund
[ERROR] Pascal Merz Pieter Meulenhoff Teemu Murtola
[ERROR] Szilard Pall Sander Pronk Roland Schulz
[ERROR] Michael Shirts Alexey Shvetsov Alfons Sijbers
[ERROR] Peter Tieleman Jon Vincent Teemu Virolainen
[ERROR] Christian Wennberg Maarten Wolf Artem Zhmurov
[ERROR] and the project leaders:
[ERROR] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[ERROR]
[ERROR] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[ERROR] Copyright (c) 2001-2019, The GROMACS development team at
[ERROR] Uppsala University, Stockholm University and
[ERROR] the Royal Institute of Technology, Sweden.
[ERROR] check out http://www.gromacs.org for more information.
[ERROR]
[ERROR] GROMACS is free software; you can redistribute it and/or modify it
[ERROR] under the terms of the GNU Lesser General Public License
[ERROR] as published by the Free Software Foundation; either version 2.1
[ERROR] of the License, or (at your option) any later version.
[ERROR]
[ERROR] GROMACS: gmx grompp, version 2021
[ERROR] Executable: /mnt/e/software/install/gromacs2021nompi/bin/gmx
[ERROR] Data prefix: /mnt/e/software/install/gromacs2021nompi
[ERROR] Working dir: /mnt/e/software/gromacs-2021/build/PyAutoFEP/docs/tutorial01
[ERROR] Command line:
[ERROR] gmx grompp -f /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/genion_step5_094106_01112024.mdp -c /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolvated_step4_094106_01112024.gro -p /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolv_step4_094106_01112024.top -o /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/genion_step6_094106_01112024.tpr -maxwarn 1 -po /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/mdout_step6_094106_01112024.mdp
[ERROR]
[ERROR]
[ERROR] NOTE 1 [file /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/genion_step5_094106_01112024.mdp]:
[ERROR] For a correct single-point energy evaluation with nsteps = 0, use
[ERROR] continuation = yes to avoid constraining the input coordinates.
[ERROR]
[ERROR] Generating 1-4 interactions: fudge = 0.5
[ERROR]
[ERROR] NOTE 2 [file systemsolv_step4_094106_01112024.top, line 56]:
[ERROR] System has non-zero total charge: -10.000000
[ERROR] Total charge should normally be an integer. See
[ERROR] http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
[ERROR] for discussion on how close it should be to an integer.
[ERROR]
[ERROR]
[ERROR]
[ERROR]
[ERROR] -------------------------------------------------------
[ERROR] Program: gmx grompp, version 2021
[ERROR] Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 681)
[ERROR]
[ERROR] Fatal error:
[ERROR] number of coordinates in coordinate file
[ERROR] (/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolvated_step4_094106_01112024.gro,
[ERROR] 44742)
[ERROR] does not match topology
[ERROR] (/tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolv_step4_094106_01112024.top,
[ERROR] 3930)
[ERROR]
[ERROR] For more information and tips for troubleshooting, please check the GROMACS
[ERROR] website at http://www.gromacs.org/Documentation/Errors
[ERROR] -------------------------------------------------------
[ERROR]
[ERROR]
[ERROR] ==================================================
[ERROR] This is likely caused by a failing to edit the intermediate topology file /tmp/tmpm3has1wz/tutorial/FXR_12-FXR_74/protein/build_system_094104_01112024/systemsolv_step4_094106_01112024.top. Rerunning with output_hidden_temp_dir=False may solve this issue.