AMBER Archive (2004)

Subject: AMBER: Re: AMBER

From: vidit kumar (
Date: Wed Jun 02 2004 - 20:19:08 CDT

I still have the problem. When I load my pdb file (containg 900 atoms) in xleap and click on the edit selected atom I dont see any charges assigned to them. and there is no bonding also. In the tutorial after downloading the pdb file, it says some treatment required of the pdb file (gave some reference pdb file also).
Should I run the antechamber to get the required files for Sander or another command? thanks for your help.
  ----- Original Message -----
  From: Ross Walker
  Sent: Tuesday, June 01, 2004 2:49 PM
  Subject: RE: AMBER: Amber7: pdb format file

  Dear Vidit,

  Take a look at the tutorials

  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

  |\oss Walker

  | Department of Molecular Biology TPC15 |
  | The Scripps Research Institute |
  | Tel:- +1 858 784 8889 | EMail:- |
  | | PGP Key available on request |

    From: [] On Behalf Of vidit kumar
    Sent: 01 June 2004 11:13
    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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