AMBER Archive (2008)

Subject: RE: AMBER: Initial structure from NMR structures

From: Ross Walker (
Date: Tue Aug 19 2008 - 09:05:43 CDT

Hi Siddharth,


In theory you can take any of these structures since ideally you should be
running your simulation for long enough that the results you obtain are not
a function of which of the 30 starting structures you choose. In practice
you may want to choose 5 or so and run 5 sets of simulations so you can
compare results across them.


Good luck,



From: [] On Behalf Of
Siddharth Rastogi
Sent: Monday, August 18, 2008 11:16 PM
Subject: AMBER: Initial structure from NMR structures


Dear Amber users,

My protein has NMR structures ( with 30 Models). No average NMR structure is
there. To run simulation whether I can take any one model among 30 models as
initial structure?. Kindly help me in this regard.

with thanks,

Siddharth Rastogi

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