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 Fri Mar 08 2013 - 05:00:02 PST
