During the execution of the following command:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
in Gromacs MD Simulation, I get the following result with errors.
GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /mnt/c/Users/Raphael/Desktop/Gromacs/540-GROMACS
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 919551497
WARNING 1 [file 540.prm, line 36]:
Bondtype U-B 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.
old: 124.6 391.622 0 0 124.6 391.622 0 0
new: CG2O1 NG2S1 CG2O6 5 120.000000 418.400000 0.00000000 0.00
ERROR 1 [file 540.prm, line 53]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
ERROR 2 [file 540.prm, line 60]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
ERROR 3 [file 540.itp, line 94]:
No default Bond types
ERROR 4 [file 540.itp, line 95]:
No default Bond types
ERROR 5 [file 540.itp, line 299]:
No default U-B types
ERROR 6 [file 540.itp, line 300]:
No default U-B types
ERROR 7 [file 540.itp, line 301]:
No default U-B types
ERROR 8 [file 540.itp, line 302]:
No default U-B types
ERROR 9 [file 540.itp, line 330]:
No default U-B types
ERROR 10 [file 540.itp, line 331]:
No default U-B types
ERROR 11 [file 540.itp, line 332]:
No default U-B types
ERROR 12 [file 540.itp, line 418]:
No default Proper Dih. types
ERROR 13 [file 540.itp, line 419]:
No default Proper Dih. types
ERROR 14 [file 540.itp, line 420]:
No default Proper Dih. types
ERROR 15 [file 540.itp, line 424]:
No default Proper Dih. types
ERROR 16 [file 540.itp, line 425]:
No default Proper Dih. types
ERROR 17 [file 540.itp, line 426]:
No default Proper Dih. types
ERROR 18 [file 540.itp, line 428]:
No default Proper Dih. types
ERROR 19 [file 540.itp, line 429]:
No default Proper Dih. types
ERROR 20 [file 540.itp, line 466]:
No default Proper Dih. types
ERROR 21 [file 540.itp, line 469]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type '540'
NOTE 2 [file topol.top, line 44220]:
System has non-zero total charge: -2.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
-------------------------------------------------------
Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 669)
Fatal error:
number of coordinates in coordinate file (solv.gro, 62424)
does not match topology (topol.top, 4731)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
PLEASE I NEED A SOLUTION TO THIS ERROR AS SOON AS POSSIBLE. I AM ALSO NEW TO GROMACS MD SIMULATION.
THE ATTACHED FILES ARE PICTURES OF THE ERROR AND ALSO THE solv.gro and topol.top
THANKS
When running your command line you must ensure you add the number of atoms copied from coordinate section of ligand.gro to the existing number of atoms in complex.gro e.g. if complex.gro has 2700 atoms and ligand.gro has 35 the total becomes 2735. You have to change the number in the 2nd line of complex.gro to 2735.
Then you have to include the parameters of ligand.itp to your topol.top file i.e.
; Include ligand topology
#include "ligand.itp"
just below the posre.itp
Include ligand.prm into topol.top as well just above the molecule type i.e.
; Include ligand parameters
#include "ligand.prm"
Ahmed Adebayo Ishola I did all that before getting the errors you see above.
@Raphael onuku, you missed some lines that's why u are getting the error
http://manual.gromacs.org/documentation/2018.1/user-guide/run-time-errors.html
Before preparing the file ions.tpr making changes in the topol.top file might help in solving the error.
STEP1: Change the last line of topol.top to
540 1
SOL 19231
STEP2:Use the command line and convert the file using
$ dos2unix topol.top
STEP3:Finally prepare the ions.tpr
This error occurred because you did some mistake from previous steps or system clearly not defined.
The topol.top file containing all the molecular information which is not match with the solvent gro file.
Two way it can solve
1. Solution: Go to your topol.top file and scroll down to the end where you will find the number of SOL molecules.
Simply increase or decrease the number according to your situation but remember, changing 1 number counts for 3(1 molecule count as 3 in solv.gro). So, you have increased or decreased number of solution in topol.top file and it worked.
2.If you go through gromacs documantion or mail group;you will find some pdb2gmx error solution information.
I suggested, please check your protein co-ordinate file, complex.gro file and topology building commands again. I hope you will find some hint to solve this problem.
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