[gmx-users] Hydrogen duplication

mkrzemin at nmr.chem.uu.nl mkrzemin at nmr.chem.uu.nl
Wed Jan 19 14:54:33 CET 2005

Hi gmx users,

I have a trouble after generating a gro file and itp file thanks to
pdb2gmx. I need to perform a dynamic with a protein inside which is a
non-regular residue. I set up this residue in the topology file (*.rtp)
and int eh .hdb file (for hydrogens). One moiety of this residue contains
a adenine with a NH2.
Actually, some Hydrogens are duplicated in the itp file at the level of
this NH2 of the adenine. The duplicated Hydrogens have got the same
coordinates than the first ones.

Help would be appreciated.

Thanks in advance,
Mickaël Krzeminski

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