('binary' encoding is not supported, stored as-is)
Dear Amber Community,
I ran an MD of a polymer in explicit solvent. I ran the simulation in
several parts for a total of 3 nanoseconds. The version of Amber I am
using is Amber7.
When putting these trajectories through ptraj to get a complete
trajectory from 20 ps to 3ns, one of the trajectories turned out to be
corrupted. It simply stopped reading in this trajectory, stated that it
was corrupted and went to the next trajectory. That basically looked like this:
Set 300 . . . . . . . . . . . . . . . . . . . . . . . . .
Set 350 . . . . . . . . . . . . . . . . . . . . . . . . .
Set 400
Processing AMBER trajectory file g224_solv_bio_md5.mdcrd
Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500 ...........................
ERROR in readAmberTrajectory(): Set #528 is corrupted ( 40)...
Processing AMBER trajectory file g224_solv_bio_md6.mdcrd
Set 1 .................................................
When looking at the trajectory in question in moil-view the trajectory is
fine to frame 527. Frame 528 the bonds get all jumbled up, similar to
when the wrong topology file is used with the wrong coordinates.
The next trajectory file is fine again, and can be viewed through moil-view.
Can this be fixed somehow? Or do I need to run everything starting from
that frame 528 onwards again?
Any suggestions or explantions?
Best Regards,
Armin
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Oct 28 2004 - 19:53:00 PDT
