AMBER Archive (2008)

Subject: AMBER: protonate in Amber10

From: Benjamin Juhl (
Date: Wed May 28 2008 - 09:55:06 CDT


i wanted to use protonate on a pdb file, but the outputfile was always
empty. That is if i used the protonate from amber10 - if i use protonate
from amber9 everthing works fine.

Commands used:
/share/apps/amber10/exe/protonate -k -m -i 1CRLA.pdb -o 1CRLA_prot.pdb
  7922 atoms read from file
 This version only dimensioned for 30000 atoms!

1CRLA_prot.pdb is an empty file.
(adding the -f option doesn't change anything)

However if i do the same with the old protonate from amber9 it works fine
/share/apps/amber9_ompi/exe/protonate -k -m -i 1CRLA.pdb -o 1CRLA_prot.pdb

After this, 1CRLA_prot.pdb is a pdb file with all the needed protons.

Both versions were compiled with the same pathscale compiler suite
(2.5). For Amber10, all bugfixes up to bugfix 5 were applied.
I think the problem must be with the pdb file, because for other pdb
files protonate adds the required hydrogens without problems. Yet i do
not understand why it runs smoothly with the old version but not at all
with the new one. Were there changes in the accepted formats?

Benjamin Juhl

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