AMBER Archive (2009)

Subject: AMBER: apparent error in closest function in ptraj 10

From: Roman Osman (
Date: Fri Jan 02 2009 - 09:54:48 CST

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

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