How to correct fatal errors in Gromacs 2020.6?

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1

GROMACS version: 2020.6
GROMACS modification: No
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Command line:

gmx_mpi grompp -f ions.mdp -c solvate.pdb -p -o ions.tpr -maxwarn 3

ERROR 83 [file topol.top, line 15255]:
atom H21 (Res LIG-1) has mass 0 (state A) / 0 (state B)

ERROR 84 [file topol.top, line 15255]:
atom H22 (Res LIG-1) has mass 0 (state A) / 0 (state B)

ERROR 85 [file topol.top, line 15255]:
atom C23 (Res LIG-1) has mass 0 (state A) / 0 (state B)

ERROR 86 [file topol.top, line 15255]:
atom H29 (Res LIG-1) has mass 0 (state A) / 0 (state B)

There were 2 notes

There were 3 warnings

Program: gmx grompp, version 2020.6
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2070)

Fatal error:
There were 86 errors in input file(s)

Fatal error:

There were 86 errors in input file(s)

Last 4 error lines are only showed because other 82 error lines are similar with this 4 error lines

Thanks in advance

3

Hi,
it looks like that something is wrong with your topology files. I guess residue LIG-1 is a ligand. You can check that all the parameters and masses of LIG-1 are properly defined.
Best regards
Alessandra