AMBER Archive (2009)

Subject: [AMBER] How to introduce the second protein molecule into simulation box?

From: Siddharth Rastogi (siddharthrastogi08_at_gmail.com)
Date: Fri Oct 16 2009 - 02:00:03 CDT

Dear Amber users,I have x ray crystal structure for the monomer of a
 protein. This protein is well known for aggregation. I am interested to
check aggregation tendency of this protein. so I want to start with two
molecules of this protein. My question is how to introduce the second
protein molecule into the simulation box?. I have in my mind to use chimera
and open the same pdb file twice and then translate one model to certain
distance and then write pdb for two models into a single file. And use this
file in xleap to get top and crd files. Whether this is ok?. can any one
help me in this regard.

with regards and thanks,
Siddharth Rastogi
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