AMBER: protonate

From: Gustavo Pierdominici Sottile <>
Date: Fri, 14 Jan 2005 15:05:49 -0300

Hi: Im 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
  -f traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
  -n index.ndx Input, Opt. Index file
  -o protonated.xtc Output Generic trajectory: xtc trr trj gro g96
      Option Type Value Description
      -[no]h bool no Print help info and quit
       -nice int 0 Set the nicelevel
          -b time -1 First frame (ps) to read from trajectory
          -e time -1 Last frame (ps) to read from trajectory
         -dt time -1 Only use frame when t MOD dt = first time (ps)
Unknown argument: -k
Unknown argument: -d
Unknown argument: PROTON_INFO
Unknown argument: -i
Unknown argument: p1.pdb

I am following the description that is in amber home page
(plastocyanin/ion/water). The manual, also refers to the option -k, -d -i ,
etc. But when trying to use them it appears as if only the options -s ,-f
-o,-b, etc could be used. The error should be evident, but I can not see it.
Please, if someone could help me, I would be grateful
Thanking in advance

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Received on Fri Jan 14 2005 - 18:52:59 PST
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