[AMBER] [Fwd: Re: pre-processing of trajectories]

From: <moitrayee.mbu.iisc.ernet.in>
Date: Thu, 24 Jun 2010 12:51:16 +0530 (IST)

------------------------------- Original Message -------------------------------
Subject: Re: [AMBER] pre-processing of trajectories
From: moitrayee.mbu.iisc.ernet.in
Date: Thu, June 24, 2010 12:50 pm
To: "AMBER Mailing List" <amber.ambermd.org>
--------------------------------------------------------------------------------

Thanks a lot for the reply.
When I view my trajectories in VMD, the dimeric protein moves to different
position within the solvent box but does not come out of the box or the system
does not 'break-up'. When I check for equillibrium using standard parameters
mentioned in the tutorial such as total enegy, density, temp, etc and also rmsd
and radius of gyration, an equilibrium seems to have been reached. However, when
I do PCA using ptraj and plot the projections on the top components, it
fluctuates rapidly as shown in the figure attached, one reason for which can be
the periodic imaging artefact. When I do center and image the plots attached
improves and shows equillibration with the projections being distributed around
a mean value. But if there is no imaging artefact, why should this happen at
all?

Please help me regarding this problem.

Sincere Regards,
Moitrayee

> 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 Thu Jun 24 2010 - 00:30:05 PDT
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