I believe it is all depending on what is your purpose. Some will just do
minimisation explicitly on the structure using NMR constraint using the
input file from DYANA, CYANA structure. So that the structure deposited into
PDB data bank would be energy minimised structure. Some would do
minimisation followed by MD and minimisation using the same DYANA/CYANA
structure. Others would also build the structure from the scratch and do MD
with constraint and followed by minimisation with constraint to get the
energy minimised structure. Hope this help a little bit. If you are not
after the energy minimised structure, then don't worry about minimisation
after the MD.
Andy
On 8/29/07, Prem Prakash Pathak <prempolymer.gmail.com> wrote:
>
> Dear AMBER user,
> What do we mean by refinement of struture using amber?
>
> Will any one explain me, what are the step followed to refine an NMR
> structure using AMBER?
> Does refinement means, minimization using the NMR constraint,
> or it includes the molecular simulation using the NMR constraints?
>
> PREM
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Received on Sun Sep 09 2007 - 06:07:05 PDT
