[gmx-users] Error in protonating ASP in pdb2gmx.

Gerrit Groenhof G.Groenhof at chem.rug.nl
Thu Dec 5 12:56:15 CET 2002

> Hi to all,
> I need to have ASP protonated (charge = 0), so I chose -asp
> option in pdb2gmx, then I specified ASP I wanted to be protonated. 
> pdb2gmx added proton named HD1, which is not listed in the
> ffgmx2.rtp:[ASPH] file and I receive error message:
> "Fatal error: Atom HD1 not found in rtp database in residue ASPH,
> it looks a bit like HD2"
> There exist only HD2 in rtp. Why pdb2gmx don't use this one instead? 

You can just change the OD1 to OD2 and vice versa and name the HD1 HD2
in the pdb file

Good luck,


> Greetings, Martin.
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