Re: [AMBER] Regarding centering a tetrameric molecule

From: <dilrajl.bii.a-star.edu.sg>
Date: Mon, 11 Mar 2013 14:50:16 +0800

Dear jason,
            Thank you for your response. Well I tried the autoimage
option from cpptraj but the problem still persists. Here is the input
file I have used.

autoimage
center :1-396 mass origin
image origin center
rmsd first :1-396.N,CA,C

Just to clarify the issue further, I am attaching two image files here
to demonstrate the orientation change I was referring to in going from
one snap shot to the next. One can clearly see the rearrangement
taking place.

Matter of fact I have also tried the second option that you have
suggested that of centering the monomers one at a time. Here is the
input file for that.

center :1-184 mass origin
image origin center
center :1-198 mass origin
image origin center
center :1-382 mass origin
image origin center
center :1-396 mass origin
image origin center
rms first :1-396 .N,CA,C

This also doesn't solve the issue at hand.

Can you please suggest me anything that I can work out.

Thank you,
Dilraj.


Quoting dilrajl.bii.a-star.edu.sg:

> Dear Amber users,
> I have a query regarding centering of a tetrameric
> molecule during post processing of a simulated trajectory. I will be
> glad if you can kindly provide me with some insights on the problem
> that I am currently encountering in this regard.
>
> I have done simulation of a tetrameric complex in explicit water.
> After completing the simulation, I want to recenter the molecule
> into the primary box. The total number of residues in the complex is
> 396 and each monomer comprises of the following residue set.
> (monomer-1: 1-184, monomer-2: 185-198, monomer-3: 199-382 and
> monomer-4: 383-396.
>
> SO for re-centering, I used the following command.
>
> trajin prod.mdcrd
> center :1-184 mass origin
> image origin center
> center :1-396 mass origin
> image origin center
> rms first :1-396.N,CA,C
> strip :WAT
> strip:Cl-
> trajout prod_cen.mdcrd
>
> Now after this, when I visualize the trajectory in VMD, I observe
> that initially the trajectory is fine but later on, there are sudden
> fluctuations in the orientation of the molecules. I believe this has
> got something to do with the re-centering scheme I am using since
> the simulations have progressed fine.
>
> I am not sure If I have been clear enough with my description.
>
> Please let me know and will be glad to get some inputs.
>
> Thank you,
> Dilraj.




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Received on Mon Mar 11 2013 - 00:00:02 PDT
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