Unknown error! Could not convert string "if" to float64 at row 0, colum 1

[Tangbbmc]

Running post-treatment reported a error mentioned above.

[HanatoK]

@Tangbbmc
You need to run the shell scripts (.sh files) following the Readme.txt to calculate the PMFs, and then select the PMFs in the Post-treatment tab in BFEE2 to estimate the binding free energy. The .sh files are not expected to be used for post-treatments.

[Tangbbmc]

Ok! Thanks for your reply. Do these shell scripts need be be run manually step by step? I run the first shell script, namely 000_eq/000_generate_tpr.sh. However, there are six warnnings. See below. ***@***.***:~/Videos/BFEE/000_eq$ bash 000_generate_tpr.sh Will use the gromacs executable binary at /usr/local/gromacs/bin/gmx Making gromacs tpr file (000_eq.tpr)... :-) GROMACS - gmx grompp, 2020.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2020.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/twg/Videos/BFEE/000_eq Command line: gmx grompp -f 000_eq.mdp -c ../Protein/p41-abl.pdb.new.gro -p ../Protein/p41-abl.top -o 000_eq.tpr -po 000_eq.mdp WARNING 1 [file 000_eq.mdp, line 320]: Unknown left-hand 'mts' in parameter file WARNING 2 [file 000_eq.mdp, line 320]: Unknown left-hand 'sc-function' in parameter file WARNING 3 [file 000_eq.mdp, line 320]: Unknown left-hand 'sc-gapsys-scale-linpoint-lj' in parameter file WARNING 4 [file 000_eq.mdp, line 320]: Unknown left-hand 'sc-gapsys-scale-linpoint-q' in parameter file WARNING 5 [file 000_eq.mdp, line 320]: Unknown left-hand 'sc-gapsys-sigma-lj' in parameter file WARNING 6 [file 000_eq.mdp, line 320]: Unknown left-hand 'qmmm-cp2k-active' in parameter file Setting the LD random seed to -836543482 Generated 701 of the 703 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 703 of the 703 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'system1' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'system2' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'TIP3' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'SOD' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'CLA' turning H bonds into constraints... Analysing residue names: There are: 68 Protein residues There are: 3452 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 23268.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.232 nm, buffer size 0.032 nm Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.118 0.118 0.118 Estimate for the relative computational load of the PME mesh part: 0.18 This run will generate roughly 317 Mb of data There were 6 warnings

…

------------------------------------------------------- Program: gmx grompp, version 2020.2 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353) Fatal error: Too many warnings (6). If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- You can now run gromacs by the following example: /usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s 000_eq.tpr -deffnm output/000_eq.out -colvars 000_colvars.dat 发件人：HanatoK ***@***.***> 发送日期：2023-02-21 17:13:20 收件人：fhh2626/BFEE2 ***@***.***> 抄送人：Tangbbmc ***@***.***>,Mention ***@***.***> 主题：Re: [fhh2626/BFEE2] Unknown error! Could not convert string "if" to float64 at row 0, colum 1 (Issue #96) @Tangbbmc You need to run the shell scripts (.sh files) following the Readme.txt to calculate the PMFs, and then select the PMFs in the Post-treatment tab in BFEE2 to estimate the binding free energy. The .sh files are not expected to be used for post-treatments. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[HanatoK]

@Tangbbmc
Could you upload 000_eq.mdp?

[Tangbbmc]

@HanatoK Ok. The files I used were generated from the input files for testing BFEE2, which were provided by you (from your published paper).
000_eq.zip

[HanatoK]

@Tangbbmc
As shown in your 000_eq.mdp, it seems you have already run the .sh file on your local computer with GROMACS 2022.4, and then moved it to somewhere else with GROMACS 2020.2 to continue. The GROMACS mdp file is not backward compatible. It should be better if you can proceed all operations using the same version of GROMACS.

[Tangbbmc]

Yes. I run the .sh file on two different systems (GROMACS 2022.4 in win10 system, GROMACS 2020.2 in Ubuntu system). However, these operations failed to generate .tpr file. The following runing report was from Cygwin64 terminal in win10 system. ***@***.*** ~ $ cd /cygdrive/c/Users/tangw/Desktop/gmx_MMPBSA/BFEE2/test/pre-treatment/Gromacs/BFEE/000_eq ***@***.*** /cygdrive/c/Users/tangw/Desktop/gmx_MMPBSA/BFEE2/test/pre-treatment/Gromacs/BFEE/000_eq $ ls 000_colvars.dat 000_generate_tpr.sh output 000_eq.mdp colvars.ndx reference.xyz ***@***.*** /cygdrive/c/Users/tangw/Desktop/gmx_MMPBSA/BFEE2/test/pre-treatment/Gromacs/BFEE/000_eq $ bash 000_generate_tpr.sh Will use the gromacs executable binary at /cygdrive/d/gmx2022.4/bin/gmx Making gromacs tpr file (000_eq.tpr)... :-) GROMACS - gmx grompp, 2022.4 (-: Executable: D:\gmx2022.4\bin\gmx.exe Data prefix: D:\gmx2022.4 Working dir: C:\Users\tangw\Desktop\gmx_MMPBSA\BFEE2\test\pre-treatment\Gromacs \BFEE\000_eq Command line: gmx grompp -f 000_eq.mdp -c ../Protein/p41-abl.pdb.new.gro -p ../Protein/p41-a bl.top -o 000_eq.tpr -po 000_eq.mdp Ignoring obsolete mdp entry 'ns-type' WARNING 1 [file 000_eq.mdp]: The Berendsen barostat does not generate any strictly correct ensemble, and should not be used for new production simulations (in our opinion). For isotropic scaling we would recommend the C-rescale barostat that also ensures fast relaxation without oscillations, and for anisotropic scaling you likely want to use the Parrinello-Rahman barostat. Setting the LD random seed to -272630793 Generated 701 of the 703 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 703 of the 703 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'system1' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'system2' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'TIP3' turning H bonds into constraints... Excluding 3 bonded neighbours molecule type 'SOD' turning H bonds into constraints... Executable: D:\gmx2022.4\bin\gmx.exe Data prefix: D:\gmx2022.4 Working dir: C:\Users\tangw\Desktop\gmx_MMPBSA\BFEE2\test\pre-treatment\Gromacs\BFEE\000_eq Command line: gmx mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s 000_eq.tpr -deffnm output/000_eq.out -colvars 000_colvars.dat There are: 3452 Other residues Analysing Protein... -------------------------------------------------------ter and splitting into gr Program: gmx mdrun, version 2022.4 Source file: src\gromacs\commandline\cmdlineparser.cpp (line 271) Function: void __cdecl gmx::CommandLineParser::parse(int *,char *[]) Error in user input: Invalid command-line options In command-line option -s File '000_eq.tpr' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2) Unknown command-line option -colvars For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- 发件人：HanatoK ***@***.***> 发送日期：2023-02-21 23:26:00 收件人：fhh2626/BFEE2 ***@***.***> 抄送人：Tangbbmc ***@***.***>,Mention ***@***.***> 主题：Re: [fhh2626/BFEE2] Unknown error! Could not convert string "if" to float64 at row 0, colum 1 (Issue #96) @Tangbbmc As shown in your 000_eq.mdp, it seems you have already run the .sh file on your local computer with GROMACS 2022.4, and then moved it to somewhere else with GROMACS 2020.2 to continue. The GROMACS mdp file is not backward compatible. It should be better if you can proceed all operations using the same version of GROMACS. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[HanatoK]

@Tangbbmc
It seems the new version of GROMACS warns the use of Berendsen barostats. To avoid this warning I propose to change the default barostats to Parrinello-Rahman. The new code is in #97 for review. After that we will make a new BFEE2 release to solve this issue.

For the time being, you can solve your problem by changing pcoupl = Berendsen to pcoupl = Parrinello-Rahman in all .mdp files after generating them by BFEE2.

Thanks!

[Tangbbmc]

@HanatoK Thank you for patient explanation! The 000_eq.tpr file was successfully generated using the method you suggested. Subsequently, the terminal prompted me to run this command "gmx mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s 000_eq.tpr -deffnm output/000_eq.out -colvars 000_colvars.dat". After doing that, a error "Unknown command-line option -colvars" happened. Could you tell me how to run 000_eq/000_eq.tpr? Thank you!

Running log:
GROMACS reminds you: "Your Bones Got a Little Machine" (Pixies)

You can now run gromacs by the following example:
/cygdrive/d/gmx2022.4/bin/gmx mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s 000_eq.tpr -deffnm output/000_eq.out -colvars 000_colvars.dat

tangw@DESKTOP-JLLRJL9 /cygdrive/c/Users/tangw/Desktop/gmx_MMPBSA/BFEE2/test/pre-treatment/Gromacs/BFEE/000_eq
$ /cygdrive/d/gmx2022.4/bin/gmx mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s 000_eq.tpr -deffnm output/000_eq.out -colvars 000_colvars.dat
:-) GROMACS - gmx mdrun, 2022.4 (-:

Executable: D:\gmx2022.4\bin\gmx.exe
Data prefix: D:\gmx2022.4
Working dir: C:\Users\tangw\Desktop\gmx_MMPBSA\BFEE2\test\pre-treatment\Gromacs\BFEE\000_eq
Command line:
gmx mdrun -ntmpi 1 -ntomp 4 -nb gpu -pme gpu -gpu_id 0 -s 000_eq.tpr -deffnm output/000_eq.out -colvars 000_colv
ars.dat

---

Program: gmx mdrun, version 2022.4
Source file: src\gromacs\commandline\cmdlineparser.cpp (line 271)
Function: void __cdecl gmx::CommandLineParser::parse(int *,char *[])

Error in user input:
Invalid command-line options
Unknown command-line option -colvars

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

[HanatoK]

@Tangbbmc
Your GROMACS build doesn't support Colvars, which is required to perform the necessary PMF calculations. Please refer to https://github.com/Colvars/colvars/#gromacs-colvars-releases for more information.

[Tangbbmc]

OK. I see, thanks for your reply! 发件人：HanatoK ***@***.***> 发送日期：2023-02-23 18:00:39 收件人：fhh2626/BFEE2 ***@***.***> 抄送人：Tangbbmc ***@***.***>,Mention ***@***.***> 主题：Re: [fhh2626/BFEE2] Unknown error! Could not convert string "if" to float64 at row 0, colum 1 (Issue #96) @Tangbbmc Your GROMACS build doesn't support Colvars, which is required to perform the necessary PMF calculations. Please refer to https://github.com/Colvars/colvars/#gromacs-colvars-releases for more information. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>