[gmx-users] How to make the missing atom by PRODRG
X.Periole at rug.nl
Sat Apr 29 08:21:24 CEST 2006
On Fri, 28 Apr 2006 20:34:17 -0700
"raja" <raja_28 at fastmail.us> wrote:
> Hi GMXIONS,
> A hydrogen atom attached to carboxylate oxygen is
>missing in output gro
> file for a ligand produced by DUNDEE PRODRG server.
If you mean that you want to portonate (neutralize) a
group ... you can do this through pdb2gmx using the -glu
that would give you the choice of protonation state for
gl in your system.
> How to add that hydrogen manually , Is there way to do
>that in any of
> available software ?
> With thanks !
> raja_28 at fastmail.us
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