GROMACS version: 2021.2
GROMACS modification: No
According to Peter at OpenMM Gromacs is supposed to have updated atoms names for the residues in the aminoacids.trp
topology files however these are still not updated. I downloaded from ftp://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz and for instance for Methoinine MET in the aminoacids.trp
under oplsaa.ff
folder the hydrogens are not named correctly. For MET the HB hydrogens should be named HB2 and HB3 as seen here https://files.rcsb.org/ligands/view/MET.cif. But they are still labeled HB1 and HB2. Example from `oplsaa.ff’.
[ MET ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2