Hi,
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:
echo $AMBERHOME
/share/apps/amber10
/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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Received on Sun Jun 01 2008 - 06:07:12 PDT
