Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.

From: David Case <david.case.rutgers.edu>
Date: Fri, 10 Mar 2017 14:13:03 -0500

On Fri, Mar 10, 2017, Nikolay N. Kuzmich wrote:
>
> what is wrong with the proline oxygen atom of the C-tail then?

The oxygen atom in your pdb-format file is called "O1"; the PDB standard,
which is what is used in Amber libraries is "OXT". You have to edit your
pdb file and change "O1 " to "OXT".

Above is why you get this error:

Created a new atom named: O1 within residue: .R<CPRO 766>
  Added missing heavy atom: .R<CPRO 766>.A<OXT 15>

Don't be afraid to experiment: try it and see what happens.

....dac


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Received on Fri Mar 10 2017 - 11:30:02 PST
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