[gmx-users] pdb2gmx without adding missing hydrogens

Markus O Kaukonen mokaukon at cc.helsinki.fi
Mon Jun 24 16:19:05 CEST 2002

Dear All,

I have cut by hand one amino acid off my protein.

I would like to calculate forces acting on this torso.

It seems possible to get the topology of the torso using
-missing option in pdb2gmx.

However, when using
> 1: Gromacs Forcefield with all hydrogens (proteins only)
pdb2gmx tries to add hydrogen atoms in the structure and crashes because
I have cut by hand one amino acid off my protein.

Is it possible to do all hydrogen force field without
pdb2gmx adding any hydrogens ?

Cheers, Markus

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