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luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
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prepare_dual_topology.py --config_file=step2.ini #145

Open hexuhua69 opened 1 month ago

hexuhua69 commented 1 month ago

$ 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.