AMBER Archive (2006)

Subject: Re: AMBER: how to do a molecular dynamic study on a trimer

From: David A. Case (
Date: Fri Aug 11 2006 - 11:05:12 CDT

On Fri, Aug 11, 2006, Abhilash wrote:

> I have a trimer and wish to do a molecular dynamics study with it. How
> do I set up amber(amber 8.0) to recognize the three chains of the trimer
> as distinct units. It treats the trimer as a continuous unit and the
> last amino acid of the chain A is treated as being bonded to the first
> amino acid of the chain B.
> I tried to specify "OXT" and "TER" tags to specify the end of the chains
> but that does not seem to work in this case.

Add a TER card between chains in the input pdb file in indeed the correct
thing to do. You'll probably have to give details of what your pdb file looks
like, and what commands you gave to LEaP.


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