AMBER Archive (2004)

Subject: RE: AMBER: Amber7: pdb format file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 01 2004 - 13:49:31 CDT

Dear Vidit,
 
Take a look at the tutorials http://amber.scripps.edu/tutorial/index.html
 
These cover running simulations using Amber. The first one, DNA explains how
to create the necessary input files for Sander from a pdb file. This assumes
you have standard nucleic or amino acid residues. If you have non-standard
residues then you should see the Plastocyanin tutorial.
 
All the best
Ross
 
/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
vidit kumar
Sent: 01 June 2004 11:13
To: amber_at_scripps.edu
Subject: AMBER: Amber7: pdb format file

Dear all
 
I am new to Amber. I want to use Amber force field method to minimize the
energy. I have created a msi format file using Cerius2 and then saved the
file also in pdb format. when I tried to use the sander it gave me the error
message, like atom type not found. Please suggest how should I proceed?
 
-vidit kumar

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