AMBER Archive (2004)

Subject: Re: AMBER: Re: AMBER

From: Jiten (
Date: Wed Jun 02 2004 - 20:48:37 CDT


As far I know about the Cerius2, it doesnot retain the atom names of the protein and DNA. It just gives the name from 1 to ... till the last atom. I am sure the atom names in the pdb file is different from amber atom names for amino acids.

I am not sure if your system is protein only OR also contains organic molecules. If it is just protein, the atom names in your pdb file is defective, meaning it is different than what had been defined by the amber. If your structure is not cystal structure (modelled by yourself), the best way to solve this problem is that have only the backbone coordinates of the protein and let the xleap add the side chains.

If you are having organic polymers or organic molecules in your system, you need to make prep file for your own. The atom names in the prep file and with that of the pdb should be same, otherewise you will face the same problem again.

You need to read some of the references on the development of amber force fields.

I hope it helps,

  ----- Original Message -----
  From: vidit kumar
  Sent: Thursday, June 03, 2004 10:19 AM
  Subject: AMBER: Re: AMBER

  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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