I guess this must come from Gromacs, which is now included in many linux
distro by default.
Mingfeng
On Fri, Jan 14, 2005 at 10:36:35AM -0800, David A. Case wrote:
> On Fri, Jan 14, 2005, Gustavo Pierdominici Sottile wrote:
>
> > Hi: I?m writing because when using the command protonate the following
> > message appears:
> > Option Filename Type Description
> > ------------------------------------------------------------
> > -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96
> > pdb
> > xml
> > -f traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
> > pdb
> > -n index.ndx Input, Opt. Index file
> > -o protonated.xtc Output Generic trajectory: xtc trr trj gro g96
> > pdb
> > Option Type Value Description
> > ------------------------------------------------------
>
> ....etc.
>
> You are running some other program that is called "protonate"; the Amber
> version doesn't look anything like the above.
>
> Try the command "which protonate" to see what you are running. To get the
> Amber one, explicitly call $AMBERHOME/exe/protonate.
>
> ...dac
>
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--
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Received on Tue Jan 18 2005 - 16:53:00 PST
