[gmx-users] Hydrogen duplication

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 19 16:01:28 CET 2005

On Wed, 2005-01-19 at 14:54 +0100, mkrzemin at nmr.chem.uu.nl wrote:
> 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.
check specification in the manual, chapter 5. You can make Hs on an NH2
with one line in the hdb file.
> Help would be appreciated.
> Thanks in advance,
> Mickaël Krzeminski
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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