Re: [gmx-users] Gromacs bug related to rms and atommass.dat interplay (Can not find mass in database for atom MG in residue)

On 2/5/20 4:58 AM, Vedat Durmaz wrote: Hi there, I'm pretty sure it's not a feature but a bug which I've faced in the GMX versions 2018.7, 2019.5 an 2020. When I try to calculate RMSD values for a protein system including a catalytic magnesium ion "Mg" using the command gmx rms -s mol.pdb -f

[gmx-users] Gromacs bug related to rms and atommass.dat interplay (Can not find mass in database for atom MG in residue)

Hi there, I'm pretty sure it's not a feature but a bug which I've faced in the GMX versions 2018.7, 2019.5 an 2020. When I try to calculate RMSD values for a protein system including a catalytic magnesium ion "Mg" using the command gmx rms -s mol.pdb -f mol.xtc -f2 mol.xtc -o mol-rmsd.xvg -debu