:-) GROMACS - gmx genion, 2022.3-plumed_2.8.1 (-:
Executable: /home/gridsan/ywang3/local/gromacs-2022.3/bin/gmx
Data prefix: /home/gridsan/ywang3/local/gromacs-2022.3
Working dir: /home/gridsan/ywang3/Project/Capping/FEP_test/test_genion
Command line:
gmx genion -s genion_step5_174735_17042023.tpr -p new.top -o fullsystem_174735_17042023.pdb -pname Na+ -nname Cl- -conc 0 -neutral
Reading file genion_step5_174735_17042023.tpr, VERSION 2022.3-plumed_2.8.1 (single precision)
Reading file genion_step5_174735_17042023.tpr, VERSION 2022.3-plumed_2.8.1 (single precision)
Will try to add 2 Na+ ions and 0 Cl- ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 6019 elements
Group 1 ( Other) has 124 elements
Group 2 ( LIG) has 124 elements
Group 3 ( Water) has 5895 elements
Group 4 ( SOL) has 5895 elements
Group 5 ( non-Water) has 124 elements
Select a group: 3
Selected 3: 'Water'
Number of (3-atomic) solvent molecules: 1965
Processing topology
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Program: gmx genion, version 2022.3-plumed_2.8.1
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 351)
Fatal error:
No line with moleculetype 'Water' found the [ molecules ] section of file
'new.top'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
The water name in my file is WAT. I can achieve the genion without -p new.top, but once I involved this file, I encounter this problem.
I also observed that gromacs generates a tmp file temp.topzxZd1H, where in this file, below [ molecules ] is empty.
I guess there are some problems to read these files?
I also tried to use like dos2unix new.top, but it didn’t work, and I didn’t move files between OS.
“Water” is a default group that GROMACS tools recognize, but for genion, you need to explicitly refer to the [moleculetype] name of what you want to replace. So “Water” will not work in this instance. It appears from the list that SOL is the appropriate choice.
I am still confused about the logic here. My initial files (.pdb and .top) contain “LIG” (the ligands) and “WAT” (the water), which are the same as the [moleculetype] name. So if I choose the [moleculetype] name in genion, it should be “WAT”, neither “SOL” nor “Water”.
The ndx list here doesn’t show “WAT” either.
I also tried to select “SOL” when genion, but it also raise an error by:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'new.top'
This is the error if I choose WAT or SOL as the answer:
gmx genion -s genion_step5_174735_17042023.tpr -o fullsystem_174735_17042023.pdb -pname Na+ -nname Cl- -conc 0 -neutral -p fullsystem_174735_17042023.top
:-) GROMACS - gmx genion, 2022.3-plumed_2.8.1 (-:
Executable: /home/gridsan/ywang3/local/gromacs-2022.3/bin/gmx
Data prefix: /home/gridsan/ywang3/local/gromacs-2022.3
Working dir: /home/gridsan/ywang3/Project/Capping/FEP_test/test_genion
Command line:
gmx genion -s genion_step5_174735_17042023.tpr -o fullsystem_174735_17042023.pdb -pname Na+ -nname Cl- -conc 0 -neutral -p fullsystem_174735_17042023.top
Reading file genion_step5_174735_17042023.tpr, VERSION 2022.3-plumed_2.8.1 (single precision)
Reading file genion_step5_174735_17042023.tpr, VERSION 2022.3-plumed_2.8.1 (single precision)
Will try to add 2 Na+ ions and 0 Cl- ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 6019 elements
Group 1 ( Other) has 124 elements
Group 2 ( LIG) has 124 elements
Group 3 ( Water) has 5895 elements
Group 4 ( SOL) has 5895 elements
Group 5 ( non-Water) has 124 elements
Select a group: WAT
Selected 3: 'Water'
Number of (3-atomic) solvent molecules: 1965
Processing topology
-------------------------------------------------------
Program: gmx genion, version 2022.3-plumed_2.8.1
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 351)
Fatal error:
No line with moleculetype 'Water' found the [ molecules ] section of file
'fullsystem_174735_17042023.top'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
gmx genion -s genion_step5_174735_17042023.tpr -o fullsystem_174735_17042023.pdb -pname Na+ -nname Cl- -conc 0 -neutral -p fullsystem_174735_17042023.top
:-) GROMACS - gmx genion, 2022.3-plumed_2.8.1 (-:
Executable: /home/gridsan/ywang3/local/gromacs-2022.3/bin/gmx
Data prefix: /home/gridsan/ywang3/local/gromacs-2022.3
Working dir: /home/gridsan/ywang3/Project/Capping/FEP_test/test_genion
Command line:
gmx genion -s genion_step5_174735_17042023.tpr -o fullsystem_174735_17042023.pdb -pname Na+ -nname Cl- -conc 0 -neutral -p fullsystem_174735_17042023.top
Reading file genion_step5_174735_17042023.tpr, VERSION 2022.3-plumed_2.8.1 (single precision)
Reading file genion_step5_174735_17042023.tpr, VERSION 2022.3-plumed_2.8.1 (single precision)
Will try to add 2 Na+ ions and 0 Cl- ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 6019 elements
Group 1 ( Other) has 124 elements
Group 2 ( LIG) has 124 elements
Group 3 ( Water) has 5895 elements
Group 4 ( SOL) has 5895 elements
Group 5 ( non-Water) has 124 elements
Select a group: SOL
Selected 4: 'SOL'
Number of (3-atomic) solvent molecules: 1965
Processing topology
-------------------------------------------------------
Program: gmx genion, version 2022.3-plumed_2.8.1
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 351)
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'fullsystem_174735_17042023.top'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------