AMBER Archive (2006)

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

From: Abhilash (mohan.25_at_osu.edu)
Date: Fri Aug 11 2006 - 10:05:44 CDT

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.
If someone can point me in the correct direction it would be a great
help indeed.
Thanks,
Abhilash Mohan
Graduate Student
The Biophysics program
The Ohio State University

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