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luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
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Solvation Error #126

Open mudit-git opened 10 months ago

mudit-git commented 10 months ago

================== STACK INFO =================== File "/media/user/New_vol/Mudit/PyAutoFEP/workdir/prepare_dual_topology.py", line 4559, in build_data = prepare_complex_system( File "/media/user/New_vol/Mudit/PyAutoFEP/workdir/os_util.py", line 558, in wrap_trace return f(*args, **kwargs) File "/media/user/New_vol/Mudit/PyAutoFEP/workdir/prepare_dual_topology.py", line 710, in prepare_complex_system os_util.run_gmx(gmx_bin, solvate_list, '', build_files_dict['solvate_log'], File "/media/user/New_vol/Mudit/PyAutoFEP/workdir/os_util.py", line 160, in run_gmx local_print('Failed to run {} {}. Error code {}.\nCommand line was: {}\n\nstdout:\n{}\n\nstderr:\n{}' File "/media/user/New_vol/Mudit/PyAutoFEP/workdir/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 solvate. Error code 1. [ERROR] Command line was: ['gmx', 'solvate', '-cp', '/tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/system_step3_130740_18102023.gro', '-cs', 'tip4p.gro', '-o', '/tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolvated_step4_130740_18102023.gro', '-p', '/tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolv_step4_130740_18102023.top'] [ERROR] [ERROR] stdout: [ERROR] [ERROR] WARNING: Masses and atomic (Van der Waals) radii will be guessed [ERROR] based on residue and atom names, since they could not be [ERROR] definitively assigned from the information in your input [ERROR] files. These guessed numbers might deviate from the mass [ERROR] and radius of the atom type. Please check the output [ERROR] files if necessary. Note, that this functionality may [ERROR] be removed in a future GROMACS version. Please, consider [ERROR] using another file format for your input. [ERROR] [ERROR] NOTE: From version 5.0 gmx solvate uses the Van der Waals radii [ERROR] from the source below. This means the results may be different [ERROR] compared to previous GROMACS versions. [ERROR] [ERROR] ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ [ERROR] A. Bondi [ERROR] van der Waals Volumes and Radii [ERROR] J. Phys. Chem. 68 (1964) pp. 441-451 [ERROR] -------- -------- --- Thank You --- -------- -------- [ERROR] [ERROR] Adding line for 10203 solvent molecules with resname (SOL) to topology file (/tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolv_step4_130740_18102023.top) [ERROR] [ERROR] [ERROR] stderr: [ERROR] :-) GROMACS - gmx solvate, 2023.1 (-: [ERROR] [ERROR] Executable: /usr/local/bin/gmx [ERROR] Data prefix: /usr/local [ERROR] Working dir: /media/user/New_vol/Mudit/PyAutoFEP/workdir [ERROR] Command line: [ERROR] gmx solvate -cp /tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/system_step3_130740_18102023.gro -cs tip4p.gro -o /tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolvated_step4_130740_18102023.gro -p /tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolv_step4_130740_18102023.top [ERROR] [ERROR] Reading solute configuration [ERROR] Reading solvent configuration [ERROR] [ERROR] Initialising inter-atomic distances... [ERROR] Generating solvent configuration [ERROR] Will generate new solvent configuration of 5x5x3 boxes [ERROR] Solvent box contains 50244 atoms in 12561 residues [ERROR] Removed 4412 solvent atoms due to solvent-solvent overlap [ERROR] Removed 5020 solvent atoms due to solute-solvent overlap [ERROR] Sorting configuration [ERROR] Found 1 molecule type: [ERROR] SOL ( 4 atoms): 10203 residues [ERROR] Generated solvent containing 40812 atoms in 10203 residues [ERROR] Writing generated configuration to /tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolvated_step4_130740_18102023.gro [ERROR] [ERROR] Output configuration contains 44742 atoms in 10440 residues [ERROR] Volume : 351.895 (nm^3) [ERROR] Density : 1008.59 (g/l) [ERROR] Number of solvent molecules: 10203
[ERROR] [ERROR] Processing topology [ERROR] [ERROR] ------------------------------------------------------- [ERROR] Program: gmx solvate, version 2023.1 [ERROR] Source file: src/gromacs/utility/futil.cpp (line 580) [ERROR] Function: void gmx_file_rename(const std::filesystem::cxx11::path&, const std::filesystem::cxx11::path&) [ERROR] [ERROR] System I/O error: [ERROR] Failed to rename temp.top0A5cxs to [ERROR] /tmp/tmpbbn3b27f/tutorial/FXR_12-FXR_74/protein/build_system_130740_18102023/systemsolv_step4_130740_18102023.top. [ERROR] [ERROR] For more information and tips for troubleshooting, please check the GROMACS [ERROR] website at http://www.gromacs.org/Documentation/Errors [ERROR] ------------------------------------------------------- [ERROR]

I got this error while trying to set it up using the tutorial. I dont have an idea why this is happening. Moreocver, when i tried using it with GROMACS 2021.4, it did not read the grompp command. Please help me.

ShuhengH commented 4 months ago

Hi, did you solve this error? I'm experiencing the same problem.

mudit-git commented 4 months ago

Hi, I actually wasn’t able to solve the issue and just started using another package to start with FEP.

Thanks and regards, Mudit

On Fri, 10 May 2024 at 12:40 PM, Shuheng Huang @.***> wrote:

Hi, did you solve this error? I'm experiencing the same problem.

— Reply to this email directly, view it on GitHub https://github.com/luancarvalhomartins/PyAutoFEP/issues/126#issuecomment-2104028965, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCGGAJCKNR7LBRFJLVFEWUDZBRXEXAVCNFSM6AAAAAA6FBRVIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBUGAZDQOJWGU . You are receiving this because you authored the thread.Message ID: @.***>

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ShuhengH commented 4 months ago

Thanks for your reply. Do you have any recommended packages and tutorials for calculating FEP? :)

Best regards, Shuheng

mudit-git commented 4 months ago

Yes actually, you can use pmx for calculating FEP! Just look for it on google. There’s a lot of tutorials on it so you’ll be able to troubleshoot.

Thanks, Mudit

On Fri, 10 May 2024 at 2:10 PM, Shuheng Huang @.***> wrote:

Thanks for your reply. Do you have any recommended packages and tutorials for calculating FEP? :)

Best regards, Shuheng

— Reply to this email directly, view it on GitHub https://github.com/luancarvalhomartins/PyAutoFEP/issues/126#issuecomment-2104197001, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCGGAJC2UBZ5P75MLKFAYVLZBSBX3AVCNFSM6AAAAAA6FBRVIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBUGE4TOMBQGE . You are receiving this because you authored the thread.Message ID: @.***>

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ShuhengH commented 4 months ago

Hi Mudit, I think I've found a solution. Warning may be reported because of the Gromacs version. You can use --maxwarn to ignore these warnings. Besides, the temporary path always makes the program can't find the file, you can turn off the temporary path and let the file save locally. So my command is:

python ./prepare_dual_topology.py --config_file=step2.ini --gmx_bin_local=gmx_mpi --gmx_bin_run=gmx_mpi --output_hidden_temp_dir=False

Fortunately, I found that this naming line generates the correct tutorial.bin package. Hope this helps!

Best regards, Shuheng