GROMACS version:2022.5
GROMACS modification: Yes/No
Here post your question: During performing the MD Simulation of pdb:4xkx in GROMACS 2022.5. We selected AMBER03 Force Field & SPC Water model It is showing error during generating ION.tpr file
ERROR IS:
(base) master01@master01-HP-Z640-Workstation:~/Desktop/MD_GROMACS/MD_GROMACS_6$ gmx grompp -f ions.mdp -c box_sol.gro -p topol.top -o ION.tpr
:-) GROMACS - gmx grompp, 2022.5 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/master01/Desktop/MD_GROMACS/MD_GROMACS_6
Command line:
gmx grompp -f ions.mdp -c box_sol.gro -p topol.top -o ION.tpr
NOTE 1 [file ions.mdp]:
For a correct single-point energy evaluation with nsteps = 0, use
continuation = yes to avoid constraining the input coordinates.
Setting the LD random seed to -134223233
WARNING 1 [file LIG.itp, line 9]:
Atomtype CB was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 2 [file LIG.itp, line 11]:
Atomtype F was defined previously (e.g. in the forcefield files), and has
now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 3 [file LIG.itp, line 13]:
Atomtype CR was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2691 of the 2701 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘LIG’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 53544]:
System has non-zero total charge: -7.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
NOTE 3 [file topol.top, line 53544]:
The bond in molecule-type Protein_chain_A between atoms 192 OG and 193 HG
has an estimated oscillational period of 9.0e-03 ps, which is less than
10 times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Analysing residue names:
There are: 363 Protein residues
There are: 1 Other residues
There are: 12152 Water 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 rest is 90051.00
NOTE 4 [file ions.mdp]:
NVE simulation with an initial temperature of zero: will use a Verlet
buffer of 10%. Check your energy drift!
NOTE 5 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 3 Mb of data
There were 5 notes
There were 3 warnings
Program: gmx grompp, version 2022.5
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2661)
Fatal error:
Too many warnings (3).
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 Common Errors — GROMACS webpage https://www.gromacs.org documentation
(base) master01@master01-HP-Z640-Workstation:~/Desktop/MD_GROMACS/MD_GROMACS_6$ gmx grompp -f ions.mdp -c box_sol.gro -maxwarn 2 -p topol.top -o ION.tpr
:-) GROMACS - gmx grompp, 2022.5 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/master01/Desktop/MD_GROMACS/MD_GROMACS_6
Command line:
gmx grompp -f ions.mdp -c box_sol.gro -maxwarn 2 -p topol.top -o ION.tpr
NOTE 1 [file ions.mdp]:
For a correct single-point energy evaluation with nsteps = 0, use
continuation = yes to avoid constraining the input coordinates.
Setting the LD random seed to -214961922
WARNING 1 [file LIG.itp, line 9]:
Atomtype CB was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 2 [file LIG.itp, line 11]:
Atomtype F was defined previously (e.g. in the forcefield files), and has
now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
WARNING 3 [file LIG.itp, line 13]:
Atomtype CR was defined previously (e.g. in the forcefield files), and
has now been defined again. This could happen e.g. if you would use a
self-contained molecule .itp file that duplicates or replaces the
contents of the standard force-field files. You should check the contents
of your files and remove such repetition. If you know you should override
the previous definition, then you could choose to suppress this warning
with -maxwarn.
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2691 of the 2701 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘LIG’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 53544]:
System has non-zero total charge: -7.000000
Total charge should normally be an integer.
NOTE 3 [file topol.top, line 53544]:
The bond in molecule-type Protein_chain_A between atoms 192 OG and 193 HG
has an estimated oscillational period of 9.0e-03 ps, which is less than
10 times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Analysing residue names:
There are: 363 Protein residues
There are: 1 Other residues
There are: 12152 Water 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 rest is 90051.00
NOTE 4 [file ions.mdp]:
NVE simulation with an initial temperature of zero: will use a Verlet
buffer of 10%. Check your energy drift!
NOTE 5 [file ions.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 3 Mb of data
There were 5 notes
There were 3 warnings
Program: gmx grompp, version 2022.5
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2661)
Fatal error:
Too many warnings (3).
If you are sure all warnings are harmless, use the -maxwarn option.