where is frame 340 in the original trajectories, file1 or file2?
is it the first frame in file2? that would suggest a problem combining them.
did you view the combined file using a graphical program like vmd or
moil-view? if so, did the trajectory look ok? people often do analysis
like ptraj and never actually visually check the system during the
trajectory file- you will know right away if the file is wrong, whereas
ptraj only looks for numbers and doesn't really care much about
whether some partial frame is missing, etc.
also, why are the files so big? did you strip out solvent? that
makes the analysis faster, unless you need to keep the water, but
it doesn't appear so from your ptraj input. since you didn't provide the
ptraj
input for the combining step, I don't know how you made file1_2.mdcrd
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
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*
>
>
>
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Received on Fri Oct 15 2004 - 16:53:00 PDT
