I wanted to bring to the attention of the users of AmberTools in AMBER
10 a possible bug in the function 'closest'.
I wanted to grab the the closest 5 waters to a specific residue:
closest 5 :368 # closest 5 waters to residue 368
ptraj produces a trajectory with 5 waters but they are very far away
from the residue (> 60 A).
Adding noimage to the command did not help.
The same command in ptraj in AMBER9 runs fine and produces 5 waters
that are indeed close to the residue.
I am pasting the script here:
trajin ../EQ/dr3_tg1571.6.trj.gz 1 500 5
center origin :364-378
image origin center
#strip the Na+ ions
strip :379-392
# calculate closest 5 to residue 368
closest 5 :368
trajout dr3_tg1571_368_w5_1.trj nobox
Thanks for your help,
Roman Osman
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
Tel: 212-659-8627
Fax: 212-849-2456
e-mail: roman.osman.mssm.edu
http://atlas.physbio.mssm.edu/~osmanlab
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Received on Sun Jan 04 2009 - 01:09:38 PST
