AMBER Archive (2008)

Subject: RE: AMBER: Initial structure from NMR structures

From: Ross Walker (ross_at_rosswalker.co.uk)
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,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Siddharth Rastogi
Sent: Monday, August 18, 2008 11:16 PM
To: amber_at_scripps.edu
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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