xy21hb
commented
1 year ago make sure your gmx version is consistent with PyAutoFEP's requirement
Open kong0706 opened 1 year ago
xy21hb
commented
1 year ago make sure your gmx version is consistent with PyAutoFEP's requirement
Hello, I have run the sample tutorial and everything went smoothly. When I used the command 'prepare_dual_topology. py', I encountered an error:
[ERROR] Failed to run gmx solvate. Error code 1. [ERROR] Command line was: ['gmx', 'solvate', '-cp', '/tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/system_step3_143141_10102023.gro', '-cs', 'tip4p.gro', '-o', '/tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolvated_step4_143141_10102023.gro', '-p', '/tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolv_step4_143141_10102023.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/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolv_step4_143141_10102023.top) [ERROR] [ERROR] [ERROR] stderr: [ERROR] :-) GROMACS - gmx solvate, 2022.6 (-: [ERROR] [ERROR] Executable: /home/application/gromacs/bin/gmx [ERROR] Data prefix: /home/application/gromacs [ERROR] Working dir: /home/yjkong/PyAutoFEP/docs/tutorial01 [ERROR] Command line: [ERROR] gmx solvate -cp /tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/system_step3_143141_10102023.gro -cs tip4p.gro -o /tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolvated_step4_143141_10102023.gro -p /tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolv_step4_143141_10102023.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/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolvated_step4_143141_10102023.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 2022.6 [ERROR] Source file: src/gromacs/utility/futil.cpp (line 614) [ERROR] Function: void gmx_file_rename(const char*, const char*) [ERROR] [ERROR] System I/O error: [ERROR] Failed to rename temp.topqJwmwT to [ERROR] /tmp/tmp0hjnxd5e/tutorial/FXR_12-FXR_74/protein/build_system_143141_10102023/systemsolv_step4_143141_10102023.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 don't know how to solve it. If you have any suggestions, please let me know. Thank you very much