Thanks Dan,
It works!
I wonder if there is a help for every command of ccptraj that can be used through the command line.
Best,
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
On Dec 4, 2012, at 7:00 PM, Daniel Roe wrote:
> Hi,
>
> You need to use a topology that corresponds to your stripped
> coordinates. You can easily generate one with cpptraj - I also
> recommend using autoimage in cpptraj. The cpptraj script would be:
>
> trajin protein_prod.mdcrd 1 150 1
> strip :WAT outprefix strip
> autoimage
> rms first out rmsd.out .CA,C,N
> trajout protein_prod_centered.mdcrd nobox
>
> Assuming your input topology is named something like "protein.prmtop",
> the strip command will generate a stripped topology named
> "strip.protein.prmtop", which you can then using along with your
> stripped trajectory "protein_prod_centered.mdcrd".
>
> You can also use the parmed program to create a stripped topology.
>
> Hope this helps,
>
> -Dan
>
> On Tue, Dec 4, 2012 at 8:56 AM, Fabian Glaser <fglaser.technion.ac.il> wrote:
>> Hi all,
>>
>> I am trying to center all trajectory frames after simulation, as suggested in several tutorials and manual:
>>
>> trajin protein_prod.mdcrd 1 150 1
>> trajout protein_prod_centered.mdcrd nobox
>>
>> rms first out rmsd.out .CA,C,N
>>
>> center :1-122 mass origin
>> image origin center familiar
>>
>> strip :WAT
>>
>> The rmsd looks fine, but when I run the MD movie application in Chimera with the re-centered coordinates file, the result looks horrible, the bonds of the protein are wrong and not all the frames are uploaded.
>>
>> What am I doing wrong?
>>
>> Thanks a lot in advance,
>>
>> Fabian
>>
>>
>>
>> _______________________________
>> Fabian Glaser, PhD
>> Bioinformatics Knowledge Unit,
>> The Lorry I. Lokey Interdisciplinary
>> Center for Life Sciences and Engineering
>>
>> Technion - Israel Institute of Technology
>> Haifa 32000, ISRAEL
>> fglaser.technion.ac.il
>> Tel: +972 4 8293701
>> Fax: +972 4 8225153
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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 Wed Dec 05 2012 - 00:00:03 PST
