Hi,
You can use the 'skipbadframes' keyword with the 'check' command to skip
corrupted frames. There's a few examples of how in the Amber 15 manual
(section 29.9.9, page 559).
Hope this helps,
-Dan
On Mon, Jul 27, 2015 at 4:32 AM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> Greetings,
>
> I have a long netcdf trajectory with several corrupted frames like the
> attached one. The command lines I used in cpptraj to process the
> trajectories are the following:
>
> strip !:1-162
> center :1-162 mass origin
> image origin center familiar
> trajout protein.box.noimage.nc netcdf nobox
> trajout first_frm_protein.pdb pdb onlyframes 1
>
> Residues 1-162 correspond to the protein. I have two questions in this
> regard:
> 1) Is there any simple way to detect corrupted frames with cpptraj?
> 2) Can I specify a list of frames that I want to be discarded by cpptraj
> when it reads the processed trajectory?
>
> thanks,
> Thomas
>
>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> _______________________________________________
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>
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jul 27 2015 - 06:30:03 PDT
