RE: AMBER: Tutorial #1 ptraj/sander problem

From: Ross Walker <>
Date: Thu, 12 May 2005 15:33:44 -0700

Dear Dani,
Can you send me the mdcrd file you created on your machine, (gzipped to my
own email account, not the list please). Can you also send me your output
file. I'll take a look at these and run them through ptraj on my machine and
see what I get.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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From: [] On Behalf Of
Daniela Kohen
Sent: 12 May 2005 15:03
Subject: AMBER: Tutorial #1 ptraj/sander problem

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
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
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
"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

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


Dani Kohen

Daniela Kohen
Assistant Professor
Carleton College
(507) 646 7165

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Received on Thu May 12 2005 - 23:53:00 PDT
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