Re: [AMBER] question about advanced tutorial 3

From: Juan Eiros Zamora <>
Date: Fri, 10 Jul 2015 11:30:29 +0100


You can do that manually with any text editor. Select the corresponding
lines for ras and save them in a new file called ras.pdb, then do the
same for the raf region. Look for the TER lines in the original pdb
file, that indicates the end of a list of ATOM or HETATM records for a
chain (each of the two proteins in this case).

For more information on the pdb file format, see here


On 10/07/15 11:12, Mohsen Zakeri wrote:
> Hi,
> I am a new AmberTools user and I am trying to calculate the binding energy
> of Protein-Ligand using AmberTools. In order to do that I am trying to
> learn from advanced Tutorial #3 (TUTORIAL A3: MM-PBSA
> <>). It has been
> said there that we should separate ras-raf.pdb into to 2 pdb files
> "ras.pdb" and "raf.pdb", but I do not know how I can do so, can you help me
> with this separation part? Can I do that using Amber?
> Thanks,
> -Mohsen

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Received on Fri Jul 10 2015 - 04:00:02 PDT
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