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

[Mark Abraham]

Hi,

Only if that makes a sensible model physics... But probably this is a
problem in the (user-contributed) port of amber14sb (and there are others,
including that they haven't updated the documentation files in it, so it
claims to be something else). The alpha carbon has a new type, so probably
a dihedral for HID needs further consideration for whichever N atom type.
But you'll need to look at the literature and/or consult the people who did
the port.

Mark

On Thu, Jun 30, 2016 at 12:46 PM Julian <julimoxx at gmail.com> wrote:

> 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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