AMBER Archive (2004)

Subject: AMBER: problem with protonate

From: Richard Stefl (stefl_at_mol.biol.ethz.ch)
Date: Tue Oct 05 2004 - 12:44:05 CDT

bugfix.39 to protonate (AMBER 7.0) causes that some atoms are assigned
as "mystery protons" and are removed from the output. In my case:
OH TYR 22 8.39 5.73 -5.09
HH TYR 22 8.81 6.31 -5.75
NH1 ARG 67 0.00 5.10 8.94
HH11 ARG 67 0.17 5.91 9.50
HH12 ARG 67 -0.09 4.20 9.37
NH2 ARG 67 -0.31 4.16 6.93
HH21 ARG 67 -0.31 4.23 5.91
HH22 ARG 67 -0.41 3.27 7.37

linux> protonate -p -k -d $AMBERHOME/dat/PROTON_INFO.Brook -i test.pdb -o
test.prot.pdb

Is there any workaround....?

thank you very much in advance,
Richard Stefl


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