Re: [AMBER] pre-processing of trajectories

From: <hannes.loeffler.stfc.ac.uk>
Date: Wed, 23 Jun 2010 20:41:24 +0100

You would see imaging artefacts as a "break-up" of molecules. If your protein is, however, defined as a single molecule its structure would stay intact because imaging is done one a per molecule basis. In that case you can savely skip the centering/imageing part since you want to do RMS fitting for the PCA anyway.


-----Original Message-----
From: moitrayee.mbu.iisc.ernet.in [mailto:moitrayee.mbu.iisc.ernet.in]
Sent: Wed 6/23/2010 7:21 PM
To: AMBER Mailing List
Subject: Re: [AMBER] pre-processing of trajectories
 
Thanks a lot for your reply.
How to Understand if there is a periodic imaging artefact. Would a part of my
protein break apart from the main system when I view my trajectories in VMD ?
I know it is a naive question but would be really grateful if you please clarify.

Sincere Regards,
Moitrayee


> On Wed, 23 Jun 2010 19:32:08 +0530 (IST)
> moitrayee.mbu.iisc.ernet.in wrote:
>
>> Dear Amber Users,
>>
>> I am doing PCA analysis with ptraj using Ambertools 1.4.
>>
>> I am using the following script.
>>
>> #!/bin/sh
>>
>> /soft/amber11/exe/ptraj 2zni.prm.top << EOF
>>
>> trajin 2zni.0030_0040.crd
>> trajin 2zni.0040_0050.crd
>>
>> rms first out rms .CA
>> matrix covar name 2zni_covar .CA out 2zni_covar.dat
>> analyze matrix 2zni_covar name 2zni-pca out 2zni_pcavec.dat vecs 100
>>
>> center .CA
>> image origin center
>> strip :WAT
>>
>> go
>>
>> Will this script take care of any periodic imaging artefact in the
>> system befor doing PCA?
>
> If you want that to happen you will also have to invoke the center and
> image commands BEFORE doing PCA, i.e. before the RMS fit.
>
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Received on Wed Jun 23 2010 - 13:00:03 PDT
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