AMBER Archive (2008)

Subject: AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member

From: Vidana.Epa_at_csiro.au
Date: Wed Feb 06 2008 - 00:08:19 CST

Dear Amber users,

 

            I am very interested to know what the experience in the
community has been regarding MD simulations of NMR structures: are
'minimized average structures' in PDB files better behaved (for example
smaller rmsd's from the experimental structure) than individual ensemble
members in multi-model (ensemble) PDB files (or vice versa)?

 

Thanks very much.

 

Cheers,

 

Vidana.

 

 

 

Vidana C. Epa

 

CSIRO,

Division of Molecular Health & Technologies,

343 Royal Parade,

Parkville, Victoria 3052,

AUSTRALIA.

 

tel: (61) - 3 - 9662 - 7345

fax:(61) - 3 - 9662 - 7347

 

email: Vidana.Epa_at_csiro.au

 

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