30 January 2019 3 9K Report

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.

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