AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8

From: Chris Moth <>
Date: Mon, 31 Jan 2005 15:39:56 -0600

The AMBER 7 and 8 manual .pdfs describe the -b and -c options of protonate, and
the ambpdb section of the manual also suggests use of protonate to alter proton

This may not be a software bug report - but a note that the manual is out of
sync with the package.

I think the last version of protonate that supported -b (and -c (and perhaps
others)) was AMBER 6.

Dr. Case suggested to a user that they try -b for a problem back in March of
2004 - so perhaps the removal of -b is a bug that should be explored further.

Anyway, I have checked protonate.f and see no mention of "-b". And, here is
the "options help" for protonate in Amber 8

    -f to force write of atoms found (debugging)
    -h to write ONLY hydrogens to output file
    -k to keep original coordinates of matched protons
    -m to list mismatched protons
    -p to print proton substitutions
    -r to renumber residues starting at 1
    -d to specify datafile (default is PROTON_INFO)
    -i to specify input file (default is stdin)
    -o to specify output file (default is stdout)
    -l to specify logfile (default is stderr)

Meanwhile, I am making do with ambpdb....


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Received on Mon Jan 31 2005 - 21:53:00 PST
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