Hi,
Try using just autoimage. If you would like to center with respect to the
molecule you have highlighted red, specify that region as your anchor (e.g.
'autoimage anchor <mask>'). By default cpptraj will autoimage based on the
first molecule.
-Dan
On Monday, March 11, 2013, wrote:
> 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.
>>
>
>
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Mar 11 2013 - 05:30:03 PDT
