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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'
Setting the LD random seed to 2138992126
Generated 396495 of the 396495 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 396495 of the 396495 1-4 parameter combinations
ERROR 1 [file topol.top, line 459]:
No default Bond types
ERROR 2 [file topol.top, line 1953]:
No default Angle types
ERROR 3 [file topol.top, line 1955]:
No default Angle types
ERROR 4 [file topol.top, line 1957]:
No default Angle types
ERROR 5 [file topol.top, line 1958]:
No default Angle types
ERROR 6 [file topol.top, line 1959]:
No default Angle types
ERROR 7 [file topol.top, line 1960]:
No default Angle types
ERROR 8 [file topol.top, line 2701]:
No default Ryckaert-Bell. types
ERROR 9 [file topol.top, line 2702]:
No default Ryckaert-Bell. types
ERROR 10 [file topol.top, line 2703]:
No default Ryckaert-Bell. types
ERROR 11 [file topol.top, line 2704]:
No default Ryckaert-Bell. types
ERROR 12 [file topol.top, line 2705]:
No default Ryckaert-Bell. types
ERROR 13 [file topol.top, line 2706]:
No default Ryckaert-Bell. types
ERROR 14 [file topol.top, line 2707]:
No default Ryckaert-Bell. types
ERROR 15 [file topol.top, line 2708]:
No default Ryckaert-Bell. types
ERROR 16 [file topol.top, line 2709]:
No default Ryckaert-Bell. types
ERROR 17 [file topol.top, line 2716]:
No default Ryckaert-Bell. types
ERROR 18 [file topol.top, line 2717]:
No default Ryckaert-Bell. types
ERROR 19 [file topol.top, line 2718]:
No default Ryckaert-Bell. types
ERROR 20 [file topol.top, line 2719]:
No default Ryckaert-Bell. types
ERROR 21 [file topol.top, line 2720]:
No default Ryckaert-Bell. types
ERROR 22 [file topol.top, line 2721]:
No default Ryckaert-Bell. types
ERROR 23 [file topol.top, line 2728]:
No default Ryckaert-Bell. types
ERROR 24 [file topol.top, line 2729]:
No default Ryckaert-Bell. types
ERROR 25 [file topol.top, line 2736]:
No default Ryckaert-Bell. types
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file topol.top, line 3917]:
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.
There was 1 note
-------------------------------------------------------
Program: gmx grompp, version 2022
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2156)
Fatal error:
There were 25 errors in input file(s)
If anyone can suggest how to solve this error then it would be a great help?
It probably means that some simulation parameters are missing from your force field list of parameters. Are you following the MD tutorial by Justin Lemkul? In that case, follow the steps again, you most likely missed some steps.
Yes Sir Nicola Piasentin I am following that tutorial only. In my pdb file proline is present at the end of the terminal which is causing this problem, but when I am removing that proline from my pdb file then it is running fine. But I want proline also at the end to run this successfully.
I have also tried to eliminate proline and model it with the help of pymol builder tool but it is not working. So the conclusion is presence of proline at the end terminal is causing the problem but absence of proline resolves it.
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