Dear Amber List,
I'm currently interested in simulating peptide folding using the GB method in AMBER10. I've seen recent papers in which they got excellent results (Lin and Shell 2009; Kim, Jang, Pak ; Kim Jang Pak 2007). In these cases they reduced some intrinsic GB radii (cf Geney et al 2006). Is there a simple way to change these radii in AMBER10? The only possibilities I've come up with are manually editing the prmtop or delving into the source code. Can this be done with an frcmod file or via leap?
I'd be grateful for any comments on this,
Best wishes
Peter Winn
Peter James Winn
RCUK Roberts Fellow
Centre for Systems Biology
University of Birmingham
Tel: +44 (0)121 414 8852
Fax: +44 (0)121 414 8844
p.j.winn.bham.ac.uk
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Received on Tue Jan 26 2010 - 07:30:03 PST
