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.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
vidit kumar
Sent: 01 June 2004 11:13
To: amber.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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Received on Tue Jun 01 2004 - 19:53:01 PDT
