AMBER Archive (2008)

Subject: RE: AMBER: Query

From: Ross Walker (ross_at_rosswalker.co.uk)
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
built.

 

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 (sirius.sdsc.edu) 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.

 

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
dipti lele
Sent: Saturday, July 26, 2008 11:41 PM
To: amber_at_scripps.edu
Subject: AMBER: Query

 

Hello,

    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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