I am using GROMACS2018 with amber14sc_parmbsc1 force field for simulations. I have DNA,RNA,protein,NA,MG and water in my system.
I want to analyze my trajectory. the way I have written my trajectory is that it contains only DNA, RNA, protein, NA and MG. Now when I use the following command:
gmx rms -s XXX.gro -f YYY.xtc -n index.ndx -o rms
I get the error message:
Can not find mass in database for atom MG in residue 1082 MG
Fatal error:
Masses were requested, but for some atom(s) masses could not be found in the database. Use a tpr file as input, if possible, or add these atoms to the mass database.
A point to be mentioned is that I cannot use my original tpr file for -s as it contains DNA, RNA, protein, NA, MG and SOL. hence, I used a modified gro file XXX.gro that contains only DNA, RNA, protein, NA and MG.
Make a matching .tpr file with convert-tpr by stripping out the water. If you do analysis that requires masses, always use a .tpr file.
Hi Justin, thank you for the hint. Convert-tpr worked and I agree it is always better to use .tpr file.
But I still do not understand the error message
Can not find mass in database for atom MG in residue 1082 MG
Fatal error:
Masses were requested, but for some atom(s) masses could not be found in the database. Use a tpr file as input, if possible, or add these atoms to the mass database.
There is no match for MG in the atom mass database, so either you have to add that or simply use a .tpr file, which has explicit mass information.
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