AMBER Archive (2004)

Subject: Re: AMBER: Trajectory corruption

From: Adrian E. Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Oct 15 2004 - 12:06:23 CDT

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_at_qtp.ufl.edu
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