[gmx-users] Error in ions.tpr generation

[Neha Tiwari]

Dear gmx experts,
The ligand molecule was refined and optimized using G03 calculation and
.itp was generated using the ATB server. Still, I am getting the
following error, dirctly copied from the terminal.
And I am unable to generate any extension files in GROMACS using this .itp.



$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

                      :-) GROMACS - gmx grompp, 2018.1 (-:



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GROMACS:      gmx grompp, version 2018.1

Executable:   /usr/bin/gmx

Data prefix:  /usr

Working dir:  /home/ya/Desktop/Neha/fecA/gromos

Command line:

  gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



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 49113858

Generated 165 of the 1596 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein'

Excluding 3 bonded neighbours molecule type '4JCP'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 2 [file topol.top, line 45350]:

  System has non-zero total charge: -14.000000

  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.







Removing all charge groups because cutoff-scheme=Verlet



ERROR 1 [file topol.top, line 45350]:

  atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 2 [file topol.top, line 45350]:

  atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 3 [file topol.top, line 45350]:

  atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 4 [file topol.top, line 45350]:

  atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 5 [file topol.top, line 45350]:

  atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 6 [file topol.top, line 45350]:

  atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 7 [file topol.top, line 45350]:

  atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 8 [file topol.top, line 45350]:

  atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 9 [file topol.top, line 45350]:

  atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 10 [file topol.top, line 45350]:

  atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 11 [file topol.top, line 45350]:

  atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 12 [file topol.top, line 45350]:

  atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 13 [file topol.top, line 45350]:

  atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 14 [file topol.top, line 45350]:

  atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 15 [file topol.top, line 45350]:

  atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







There were 2 notes



-------------------------------------------------------

Program:     gmx grompp, version 2018.1

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137)



Fatal error:

There were 15 errors in input file(s)



For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------



Please help.