AMBER Archive (2005)

Subject: AMBER: Tutorial #1 ptraj/sander problem

From: Daniela Kohen (dkohen_at_carleton.edu)
Date: Thu May 12 2005 - 17:03:07 CDT

Hi,
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
(http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/
index.htm)
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!!!

THANKS A LOT !

Dani Kohen

Daniela Kohen
Assistant Professor
Carleton College
(507) 646 7165

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