[gmx-users] GLUH problem

X.Periole X.Periole at rug.nl
Fri Mar 17 08:26:13 CET 2006

Dear Jason,
> I am trying to use pdb2gmx to generate files for my 
>molecules.  I have protonated GLU in it. So I am using 
>GLUH as the residue name. However the program complains 
>Fatal error: Atom HE2 in residue GLU 4 not found in rtp 
>entry with 10 atoms
>             while sorting atoms. Maybe different 
>protonation state.
>             Remove this hydrogen or choose a different 
>protonation state.
>             Option -ignh will ignore all hydrogens in 
>the input.
> But I do find HE2 for GLUH in ffG43a1.rtp. It seems that 
>pdb2gmx can't recongnize GLUH. I am using gromacs 3.2.1. 
>Could anyone give me any hints on this?

pdb2gmx probably do not see that GLUH is actualy GLUH and
so do not fing the atom HE2 in the definition of the GLU
residue. You have to use -ignh (to ignore hydrogens) and
protonated your GLU using odb2gmx using the option -glu.
This will give you the choice between the different
protonation states, choose the good one and the topology
will be generated. Then you can use the original
conformation with the hydrogen, it should be possible.


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