AMBER Archive (2009)

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

From: D.J. Cole (djc56_at_cam.ac.uk)
Date: Fri Jan 02 2009 - 10:06:01 CST

Dear Roman,

Can you try modifying your script to read:

closest 5 :368 oxygen

so that only the distances to the water O atoms are considered. I found
that this solved the problem for me. Although it looks like there may still
be a bug there somewhere.

Danny

On Jan 2 2009, Roman Osman wrote:

>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_at_mssm.edu
> http://atlas.physbio.mssm.edu/~osmanlab
>
>

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