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.