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
nomenclature.
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....
Thanks
C
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jan 31 2005 - 21:53:00 PST
