[gmx-users] Treatment of HIE, HID, HIP with the Amber force field

Julian julimoxx at gmail.com
Thu Jun 30 12:46:35 CEST 2016


Dear Gromacs users,

I am running Gromacs using the amber14sb force field. Amber distinguishes
histamine residues according to their protonation state into HIE, HID, and
HIP.
But then Gromacs complains for HID residues: No default Improper Dih. types
Do I have to do something additional or should I just discard the different
protonation states and rename all HID to HIE?

gmx pdb2gmx -f xxx.pdb -p xxx.top -ff amber14sb -water tip3p -ignh
gmx grompp -f xxx.mdp -c xxx.pdb -p xxx.top -o xxx.tpr

Thanks for your answers!


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