AMBER Archive (2004)

Subject: AMBER: Trajectory corruption

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Oct 15 2004 - 08:48:50 CDT

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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