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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Bug-gmx_MMPBSA]: Error in the calculation of standard deviation #218

Closed jssantiago3 closed 2 years ago

jssantiago3 commented 2 years ago

Bug summary

Hi! I'm getting the following error in one of my runs.

Terminal output INFO ] Parsing results to output files... File "/home/josh/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 112, in gmxmmpbsa app.parse_output_files() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1059, in parse_output_files self.calc_types.normal[key]['delta'] = BindingStatistics(self.calc_types.normal[key]['complex'], File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 810, in __init__ self._delta() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 838, in _delta self[key] = temp.corr_sub(self.lig[key]) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 89, in corr_sub comp_std = get_corrstd(self_std, other_std) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 133, in get_corrstd return sqrt(val1 ** 2 + val2 ** 2 - 2 * val1 * val2) ValueError: math domain error Exiting. All files have been retained. Traceback (most recent call last): File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 360, in get_data self.parent.read_data(queue, self.options) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py", line 989, in read_data gmx_mmpbsa_api.load_file(path) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 78, in load_file self._get_fromApp(fname) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 376, in _get_fromApp app.parse_output_files() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1059, in parse_output_files self.calc_types.normal[key]['delta'] = BindingStatistics(self.calc_types.normal[key]['complex'], File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 810, in __init__ self._delta() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 838, in _delta self[key] = temp.corr_sub(self.lig[key]) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 89, in corr_sub comp_std = get_corrstd(self_std, other_std) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 133, in get_corrstd return sqrt(val1 ** 2 + val2 ** 2 - 2 * val1 * val2) ValueError: math domain error Aborted (core dumped)

Any idea on what could be causing this error? Thanks!

Terminal output

Terminal output ```bash INFO ] Parsing results to output files... File "/home/josh/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 112, in gmxmmpbsa app.parse_output_files() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1059, in parse_output_files self.calc_types.normal[key]['delta'] = BindingStatistics(self.calc_types.normal[key]['complex'], File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 810, in __init__ self._delta() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 838, in _delta self[key] = temp.corr_sub(self.lig[key]) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 89, in corr_sub comp_std = get_corrstd(self_std, other_std) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 133, in get_corrstd return sqrt(val1 ** 2 + val2 ** 2 - 2 * val1 * val2) ValueError: math domain error Exiting. All files have been retained. Traceback (most recent call last): File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 360, in get_data self.parent.read_data(queue, self.options) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py", line 989, in read_data gmx_mmpbsa_api.load_file(path) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 78, in load_file self._get_fromApp(fname) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 376, in _get_fromApp app.parse_output_files() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1059, in parse_output_files self.calc_types.normal[key]['delta'] = BindingStatistics(self.calc_types.normal[key]['complex'], File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 810, in __init__ self._delta() File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 838, in _delta self[key] = temp.corr_sub(self.lig[key]) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 89, in corr_sub comp_std = get_corrstd(self_std, other_std) File "/home/josh/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 133, in get_corrstd return sqrt(val1 ** 2 + val2 ** 2 - 2 * val1 * val2) ValueError: math domain error Aborted (core dumped) ``` ### gmx_MMPBSA.log [INFO ] Starting gmx_MMPBSA v1.5.2 [DEBUG ] WDIR : /home/josh/Thesis_Production_Runs/BNNT_1010_Surface/BNNT_AFB1 [DEBUG ] AMBERHOME : /home/josh/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/josh/miniconda3/envs/gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:25:59) [GCC 10.3.0] [DEBUG ] MPI : /home/josh/miniconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.3+10.ga195c7e [DEBUG ] OS PLATFORM : Linux-5.16.11-76051611-generic-x86_64-with-glibc2.34 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #202202230823~1646248261~21.10~2b22243 SMP PREEMPT Wed Mar 2 20: [DEBUG ] OS PROCESSOR : x86_64 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs sys.pdb -ci index_system.ndx -cg 2 3 -ct md_noPBC.xtc -cp topol.top -nogui [DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |;Sample input file for MMPBSA &general [DEBUG ] | [DEBUG ] |&general [DEBUG ] |sys_name="BNNT-FB1" [DEBUG ] |startframe=1 [DEBUG ] |endframe=201 [DEBUG ] |interaction_entropy=1, ie_segment=25, temperature=300 [DEBUG ] |PBRadii = 7 [DEBUG ] |/ [DEBUG ] |PB input: [DEBUG ] |&pb [DEBUG ] |radiopt=0, istrng=0.100, fillratio =4.0, inp =1 [DEBUG ] |/ [DEBUG ] |-------------------------------------------------------------- [DEBUG ] [INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/josh/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/josh/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/josh/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/josh/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [INFO ] Checking external programs...Done. [INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [DEBUG ] Running command: echo name 2 GMXMMPBSA_REC\n name 3 GMXMMPBSA_LIG\n 2 | 3\n q\n | /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index_system.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx make_ndx, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx make_ndx, version 2021.3-bioconda [DEBUG ] Executable: /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/josh/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/josh/Thesis_Production_Runs/BNNT_1010_Surface/BNNT_AFB1 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index_system.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Rockets are cool. There's no getting around that." (Elon Musk) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] Counted atom numbers up to 31509 in index file [DEBUG ] [DEBUG ] 0 System : 31509 atoms [DEBUG ] 1 Other : 431 atoms [DEBUG ] 2 BNT : 396 atoms [DEBUG ] 3 LIG : 35 atoms [DEBUG ] 4 NA : 20 atoms [DEBUG ] 5 CL : 20 atoms [DEBUG ] 6 Water : 31038 atoms [DEBUG ] 7 SOL : 31038 atoms [DEBUG ] 8 non-Water : 471 atoms [DEBUG ] 9 Ion : 40 atoms [DEBUG ] 10 BNT : 396 atoms [DEBUG ] 11 LIG : 35 atoms [DEBUG ] 12 NA : 20 atoms [DEBUG ] 13 CL : 20 atoms [DEBUG ] 14 Water_and_ions : 31078 atoms [DEBUG ] 15 BNT_LIG : 431 atoms [DEBUG ] [DEBUG ] nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups [DEBUG ] 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues [DEBUG ] 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help [DEBUG ] 'r': residue 'res' nr 'chain' char [DEBUG ] "name": group 'case': case sensitive 'q': save and quit [DEBUG ] 'ri': residue index [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] > [DEBUG ] Copied index group 2 'GMXMMPBSA_REC' [DEBUG ] Copied index group 3 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 396 35 -> 431 [DEBUG ] [DEBUG ] 16 GMXMMPBSA_REC_GMXMMPBSA_LIG: 431 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group 2_3 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx editconf -f sys.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb [DEBUG ] :-) GROMACS - gmx editconf, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx editconf, version 2021.3-bioconda [DEBUG ] Executable: /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/josh/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/josh/Thesis_Production_Runs/BNNT_1010_Surface/BNNT_AFB1 [DEBUG ] Command line: [DEBUG ] gmx editconf -f sys.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb [DEBUG ] [DEBUG ] [DEBUG ] Select a group for output: [DEBUG ] Group 0 ( System) has 31509 elements [DEBUG ] Group 1 ( Other) has 431 elements [DEBUG ] Group 2 ( GMXMMPBSA_REC) has 396 elements [DEBUG ] Group 3 ( GMXMMPBSA_LIG) has 35 elements [DEBUG ] Group 4 ( NA) has 20 elements [DEBUG ] Group 5 ( CL) has 20 elements [DEBUG ] Group 6 ( Water) has 31038 elements [DEBUG ] Group 7 ( SOL) has 31038 elements [DEBUG ] Group 8 ( non-Water) has 471 elements [DEBUG ] Group 9 ( Ion) has 40 elements [DEBUG ] Group 10 ( BNT) has 396 elements [DEBUG ] Group 11 ( LIG) has 35 elements [DEBUG ] Group 12 ( NA) has 20 elements [DEBUG ] Group 13 ( CL) has 20 elements [DEBUG ] Group 14 ( Water_and_ions) has 31078 elements [DEBUG ] Group 15 ( BNT_LIG) has 431 elements [DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 431 elements [DEBUG ] Select a group: [DEBUG ] GROMACS reminds you: "Rockets are cool. There's no getting around that." (Elon Musk) [DEBUG ] [DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility. [DEBUG ] Read 431 atoms [DEBUG ] Volume: 320.07 nm^3, corresponds to roughly 144000 electrons [DEBUG ] No velocities found [DEBUG ] Selected 16: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] No receptor structure file was defined. Using ST approach... [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Receptor: Saving group 2 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo 2 | /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx editconf -f sys.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_REC.pdb [DEBUG ] :-) GROMACS - gmx editconf, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx editconf, version 2021.3-bioconda [DEBUG ] Executable: /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/josh/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/josh/Thesis_Production_Runs/BNNT_1010_Surface/BNNT_AFB1 [DEBUG ] Command line: [DEBUG ] gmx editconf -f sys.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_REC.pdb [DEBUG ] [DEBUG ] [DEBUG ] Select a group for output: [DEBUG ] Group 0 ( System) has 31509 elements [DEBUG ] Group 1 ( Other) has 431 elements [DEBUG ] Group 2 ( GMXMMPBSA_REC) has 396 elements [DEBUG ] Group 3 ( GMXMMPBSA_LIG) has 35 elements [DEBUG ] Group 4 ( NA) has 20 elements [DEBUG ] Group 5 ( CL) has 20 elements [DEBUG ] Group 6 ( Water) has 31038 elements [DEBUG ] Group 7 ( SOL) has 31038 elements [DEBUG ] Group 8 ( non-Water) has 471 elements [DEBUG ] Group 9 ( Ion) has 40 elements [DEBUG ] Group 10 ( BNT) has 396 elements [DEBUG ] Group 11 ( LIG) has 35 elements [DEBUG ] Group 12 ( NA) has 20 elements [DEBUG ] Group 13 ( CL) has 20 elements [DEBUG ] Group 14 ( Water_and_ions) has 31078 elements [DEBUG ] Group 15 ( BNT_LIG) has 431 elements [DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 431 elements [DEBUG ] Select a group: [DEBUG ] GROMACS reminds you: "Rockets are cool. There's no getting around that." (Elon Musk) [DEBUG ] [DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility. [DEBUG ] Read 431 atoms [DEBUG ] Volume: 320.07 nm^3, corresponds to roughly 144000 electrons [DEBUG ] No velocities found [DEBUG ] Selected 2: 'GMXMMPBSA_REC' [INFO ] No ligand structure file was defined. Using ST approach... [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal Ligand: Saving group 3 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo 3 | /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx editconf -f sys.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb [DEBUG ] :-) GROMACS - gmx editconf, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx editconf, version 2021.3-bioconda [DEBUG ] Executable: /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/josh/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/josh/Thesis_Production_Runs/BNNT_1010_Surface/BNNT_AFB1 [DEBUG ] Command line: [DEBUG ] gmx editconf -f sys.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb [DEBUG ] [DEBUG ] [DEBUG ] Select a group for output: [DEBUG ] Group 0 ( System) has 31509 elements [DEBUG ] Group 1 ( Other) has 431 elements [DEBUG ] Group 2 ( GMXMMPBSA_REC) has 396 elements [DEBUG ] Group 3 ( GMXMMPBSA_LIG) has 35 elements [DEBUG ] Group 4 ( NA) has 20 elements [DEBUG ] Group 5 ( CL) has 20 elements [DEBUG ] Group 6 ( Water) has 31038 elements [DEBUG ] Group 7 ( SOL) has 31038 elements [DEBUG ] Group 8 ( non-Water) has 471 elements [DEBUG ] Group 9 ( Ion) has 40 elements [DEBUG ] Group 10 ( BNT) has 396 elements [DEBUG ] Group 11 ( LIG) has 35 elements [DEBUG ] Group 12 ( NA) has 20 elements [DEBUG ] Group 13 ( CL) has 20 elements [DEBUG ] Group 14 ( Water_and_ions) has 31078 elements [DEBUG ] Group 15 ( BNT_LIG) has 431 elements [DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 431 elements [DEBUG ] Select a group: [DEBUG ] GROMACS reminds you: "Rockets are cool. There's no getting around that." (Elon Musk) [DEBUG ] [DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility. [DEBUG ] Read 431 atoms [DEBUG ] Volume: 320.07 nm^3, corresponds to roughly 144000 electrons [DEBUG ] No velocities found [DEBUG ] Selected 3: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected CHARMM force field topology format... [INFO ] Assigning PBRadii charmm_radii to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii charmm_radii to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii charmm_radii to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f md_noPBC.xtc -s sys.pdb -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/josh/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/josh/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/josh/Thesis_Production_Runs/BNNT_1010_Surface/BNNT_AFB1 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f md_noPBC.xtc -s sys.pdb -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc [DEBUG ] Group 0 ( System) has 31509 elements [DEBUG ] Group 1 ( Other) has 431 elements [DEBUG ] Group 2 ( GMXMMPBSA_REC) has 396 elements [DEBUG ] Group 3 ( GMXMMPBSA_LIG) has 35 elements [DEBUG ] Group 4 ( NA) has 20 elements [DEBUG ] Group 5 ( CL) has 20 elements [DEBUG ] Group 6 ( Water) has 31038 elements [DEBUG ] Group 7 ( SOL) has 31038 elements [DEBUG ] Group 8 ( non-Water) has 471 elements [DEBUG ] Group 9 ( Ion) has 40 elements [DEBUG ] Group 10 ( BNT) has 396 elements [DEBUG ] Group 11 ( LIG) has 35 elements [DEBUG ] Group 12 ( NA) has 20 elements [DEBUG ] Group 13 ( CL) has 20 elements [DEBUG ] Group 14 ( Water_and_ions) has 31078 elements [DEBUG ] Group 15 ( BNT_LIG) has 431 elements [DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 431 elements [DEBUG ] Select a group: Reading frame 0 time 90000.000 [DEBUG ] Precision of md_noPBC.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] -> frame 0 time 90000.000 Reading frame 1 time 90010.000 -> frame 1 time 90010.000 Reading frame 2 time 90020.000 -> frame 2 time 90020.000 Reading frame 3 time 90030.000 -> frame 3 time 90030.000 Reading frame 4 time 90040.000 -> frame 4 time 90040.000 Reading frame 5 time 90050.000 -> frame 5 time 90050.000 Reading frame 6 time 90060.000 -> frame 6 time 90060.000 Reading frame 7 time 90070.000 -> frame 7 time 90070.000 Reading frame 8 time 90080.000 -> frame 8 time 90080.000 Reading frame 9 time 90090.000 -> frame 9 time 90090.000 Reading frame 10 time 90100.000 -> frame 10 time 90100.000 Reading frame 11 time 90110.000 Reading frame 12 time 90120.000 Reading frame 13 time 90130.000 Reading frame 14 time 90140.000 Reading frame 15 time 90150.000 Reading frame 16 time 90160.000 Reading frame 17 time 90170.000 Reading frame 18 time 90180.000 Reading frame 19 time 90190.000 Reading frame 20 time 90200.000 -> frame 20 time 90200.000 Reading frame 30 time 90300.000 -> frame 30 time 90300.000 Reading frame 40 time 90400.000 -> frame 40 time 90400.000 Reading frame 50 time 90500.000 -> frame 50 time 90500.000 Reading frame 60 time 90600.000 -> frame 60 time 90600.000 Reading frame 70 time 90700.000 -> frame 70 time 90700.000 Reading frame 80 time 90800.000 -> frame 80 time 90800.000 Reading frame 90 time 90900.000 -> frame 90 time 90900.000 Reading frame 100 time 91000.000 -> frame 100 time 91000.000 Reading frame 110 time 91100.000 -> frame 110 time 91100.000 Reading frame 120 time 91200.000 -> frame 120 time 91200.000 Reading frame 130 time 91300.000 -> frame 130 time 91300.000 Reading frame 140 time 91400.000 -> frame 140 time 91400.000 Reading frame 150 time 91500.000 -> frame 150 time 91500.000 Reading frame 160 time 91600.000 -> frame 160 time 91600.000 Reading frame 170 time 91700.000 -> frame 170 time 91700.000 Reading frame 180 time 91800.000 -> frame 180 time 91800.000 Reading frame 190 time 91900.000 -> frame 190 time 91900.000 Reading frame 200 time 92000.000 -> frame 200 time 92000.000 -> frame 210 time 92100.000 -> frame 220 time 92200.000 -> frame 230 time 92300.000 -> frame 240 time 92400.000 -> frame 250 time 92500.000 -> frame 260 time 92600.000 -> frame 270 time 92700.000 -> frame 280 time 92800.000 -> frame 290 time 92900.000 Reading frame 300 time 93000.000 -> frame 300 time 93000.000 -> frame 310 time 93100.000 -> frame 320 time 93200.000 -> frame 330 time 93300.000 -> frame 340 time 93400.000 -> frame 350 time 93500.000 -> frame 360 time 93600.000 -> frame 370 time 93700.000 -> frame 380 time 93800.000 -> frame 390 time 93900.000 Reading frame 400 time 94000.000 -> frame 400 time 94000.000 -> frame 410 time 94100.000 -> frame 420 time 94200.000 -> frame 430 time 94300.000 -> frame 440 time 94400.000 -> frame 450 time 94500.000 -> frame 460 time 94600.000 -> frame 470 time 94700.000 -> frame 480 time 94800.000 -> frame 490 time 94900.000 Reading frame 500 time 95000.000 -> frame 500 time 95000.000 -> frame 510 time 95100.000 -> frame 520 time 95200.000 -> frame 530 time 95300.000 -> frame 540 time 95400.000 -> frame 550 time 95500.000 -> frame 560 time 95600.000 -> frame 570 time 95700.000 -> frame 580 time 95800.000 -> frame 590 time 95900.000 Reading frame 600 time 96000.000 -> frame 600 time 96000.000 -> frame 610 time 96100.000 -> frame 620 time 96200.000 -> frame 630 time 96300.000 -> frame 640 time 96400.000 -> frame 650 time 96500.000 -> frame 660 time 96600.000 -> frame 670 time 96700.000 -> frame 680 time 96800.000 -> frame 690 time 96900.000 Reading frame 700 time 97000.000 -> frame 700 time 97000.000 -> frame 710 time 97100.000 -> frame 720 time 97200.000 -> frame 730 time 97300.000 -> frame 740 time 97400.000 -> frame 750 time 97500.000 -> frame 760 time 97600.000 -> frame 770 time 97700.000 -> frame 780 time 97800.000 -> frame 790 time 97900.000 Reading frame 800 time 98000.000 -> frame 800 time 98000.000 -> frame 810 time 98100.000 -> frame 820 time 98200.000 -> frame 830 time 98300.000 -> frame 840 time 98400.000 -> frame 850 time 98500.000 -> frame 860 time 98600.000 -> frame 870 time 98700.000 -> frame 880 time 98800.000 -> frame 890 time 98900.000 Reading frame 900 time 99000.000 -> frame 900 time 99000.000 -> frame 910 time 99100.000 -> frame 920 time 99200.000 -> frame 930 time 99300.000 -> frame 940 time 99400.000 -> frame 950 time 99500.000 -> frame 960 time 99600.000 -> frame 970 time 99700.000 -> frame 980 time 99800.000 -> frame 990 time 99900.000 Reading frame 1000 time 100000.000 -> frame 1000 time 100000.000 Last frame 1000 time 100000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Humbug! Most things free-born will submit to anything for a salary" (Mr. Rochester in Jane Eyre by Charlotte Bronte) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 16: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation... [INFO ] 201 frames were processed by cpptraj for use in calculation. [INFO ] Running calculations on normal system... [INFO ] Beginning PB calculations with /home/josh/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] calculating ligand contribution... [INFO ] Parsing results to output files...

Operating system

Debian

gmx_MMPBSA Version

gmx_MMPBSA v1.5.2 based on MMPBSA version 16.0 and AmberTools 20

Python version

python --version

Installation

conda AmberTools + conda

Valdes-Tresanco-MS commented 2 years ago

Usually, this is due to the use of too few frames, but this is not the case. The error is due to the fact that in the equation 2*std1*std2 > std1^2 + std2^2. This makes the total negative and therefore the square root cannot be calculated. We must check why this happens in your case

Valdes-Tresanco-MS commented 2 years ago

Can you send me the results folder by e-mail? (You don't need to include the trajectory)

jssantiago3 commented 2 years ago

Apologies it seems my previous files with the error were re-written. I re-ran gmx_mmpbsa with increased frames from 201 > 1001 and it solved the problem.