AMBER Archive (2005)

Subject: Re: AMBER: protonate

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 14 2005 - 12:36:35 CST

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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