AMBER: Tutorial #1 ptraj/sander problem

From: Daniela Kohen <>
Date: Thu, 12 May 2005 17:03:07 -0500

I am completely new to AMBER (I bought it a few months ago) and decided
to educate myself by following the instructions of Tutorial #1 from the
Amber 2004 workshop
I have the following problem when trying to get the RSMD vs. time
results for the simulation in vacuum:
When I follow the tutorial carefully (I believe) and run ptraj on the
MD trajectory file I generated using sander I get a very different
result than when I run the same command on a trajectory I downloaded
from the website (polyAT_vac_md1_12Acut.mdcrd)
The first two values in the reported output file are
0.10 0.00000
0.20 0.24643 (these are also what I get when I run ptraj on the
trajectory I downloaded)
while the ones I get using my trajectory are
0.10 0.00001
0.20 232.70956

Also the outputs are a little different: the tutorial reports the
following line
“ERROR in readAmberTrajectory(): Set #1001 is corrupted”
but I get that only if I start from the MD trajectory that I
downloaded (not the one created when using sander in my computer)

All of these points to a problem in my sander MD trajectory. But when I
look at the summary files after running the perl script for both my
sander generated trajectory and the one I downloaded I get numbers that
are very similar. And when I inspect both trajectories using VMD they
look very alike (and I do not see anything that would result in a RMSD
of 250 amstrongs!)

Also note that I am running AMBER in a windows machine using CYGWIN and
that we run the bugfix.all script after installing AMBER 8.0 a couple
of weeks ago.

I really would appreciate any help on this matter!!!


Dani Kohen

Daniela Kohen
Assistant Professor
Carleton College
(507) 646 7165
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu May 12 2005 - 23:53:00 PDT
Custom Search