Can you tell us how many frames there where in each of file1.mdcrd and
file2.mdcrd ?
basically, is the bad frame in trial1_2.mdcrd at the bounday between the
two parts ?
Steve Seibold wrote:
> Dear AMBER group
>
> I am having some difficulties with Ptraj and trajectory files.
> 1) I have two trajectory files of a protein (file1.mdcrd and
> file2.mdcrd). When I use Ptraj to obtain two separate main-chain RMSds
> (one for file1 and one for file2), everything works fine.
>
> 2) Then I combined file1.mdcrd and file2.mdcrd, with Ptraj, to obtain
> one trajectory file called file1_2.mdcrd. The output file of this
> combining process said everything went fine..no error in any sets were
> detected. When I attempted to get the main-chain RMSd with Ptraj for
> this combined file1_2.mdcrd, I got an error saying that set #340 is
> corrupted in my file1_2.mdcrd file.
>
> I am using AMBER 7. These trajectory files are very large (GB range
> each). Could this be a problem of the size of my files? Has anyone had
> this problem before? I do have all the restrt files of the runs so I
> could make the proper trajectory files, but I am afraid of just running
> into the same problem again.
>
> Any advice??
>
>
> My input file:
>
> trajin trial1_2.mdcrd
>
> box x 51.1333056 y 50.7934380 z 72.1834321
>
> center :1-198 origin
>
> image :199-398 origin center familiar
>
> rms first mass out trial1_2all_backboneflux.txt time 5 .CA,C,N
>
> atomicfluc out trial1_2residueflux.txt :1-398 byres
>
> go
>
>
>
> The output file:
>
> Processing AMBER trajectory file trial1_2.mdcrd
>
> Set 1 .................................................
>
> Set 50 .................................................
>
> Set 100 .................................................
>
> Set 150 .................................................
>
> Set 200 .................................................
>
> Set 250 .................................................
>
> Set #340 appears corrupted (
>
> 51.133 50.793 72.183)
>
> Set 300 .......................................
>
> PTRAJ: Successfully read in 339 sets and processed 339 sets.
>
> Dumping accumulated results (if any)
>
> PTRAJ RMS: dumping RMSd vs time data
>
> PTRAJ ATOMICFLUCT: Dumping atomic positional fluctuations
>
> logout
>
>
>
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
============================================================================
To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
-- Theodore Roosevelt
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Oct 15 2004 - 18:53:01 PDT
