AMBER Archive (2008)

Subject: RE: AMBER: Query

From: Ross Walker (
Date: Sun Jul 27 2008 - 04:04:57 CDT

Hi Deepti,


I suggest that you work through the tutorials on the AMBER website. These
will explain to you simple things like why VMD is giving you a straight line
when loading a restart file (simple answer is you are selecting the wrong
file format).


As for the AMBPDB command not working - was ambertools installed on your
machine? - Do you have AMBERHOME/exe in your path? How about trying
$AMBERHOME/exe/ambpdb? If ambertools and amber was installed it is highly
unlikely that ambpdb is not there since it is one of the first things to get


As for pdbs - you could use ptraj to make yourself a pdb.


>cat foo.traj


trajin foo.rst

trajout foo.pdb



>$AMBERHOME/exe/ptraj foo.prmtop < foo.traj


You could also use Sirius ( this can read a whole range of
amber output and write many different file formats. Again there is a
tutorial on the AMBER website that shows you how to do this sort of thing.




From: [] On Behalf Of
dipti lele
Sent: Saturday, July 26, 2008 11:41 PM
Subject: AMBER: Query



    I have used amber for minimising the energy of a molecule. and want to
see the molecule. AMBPDB command is not working on my pc and the error is
that the command is not found. I have a parallel MPI version of AMBER. What
should I do to get it in the pdb format. I could nto do it using VMD it is
giving straight line there.

Could you guuide me regarding it.

Thanking you!!!!

Deepti Lele,

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