[gmx-users] Error in ions.tpr generation

[Justin Lemkul]

On 2/27/20 2:50 AM, Neha Tiwari wrote:
> 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)

Apparently your topology is incorrectly formatted and does not contain 
masses of the atoms. You will need to correct its contents.

-Justin

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