AMBER Archive (2009)

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

From: Roman Osman (roman.osman_at_mssm.edu)
Date: Fri Jan 02 2009 - 11:37:09 CST

Danny,
        Thanks; it does.
        But, I agree there must be a bug somewhere.
Rami

On Jan 2, 2009, at 11:06 AM, D.J. Cole wrote:

> 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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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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