we have done it by changing the leap source code, or writing scripts
to modify the prmtop. i don't know of any way to use a leap command to
do it.
On Tue, Jan 26, 2010 at 10:13 AM, Peter Winn <p.j.winn.bham.ac.uk> wrote:
>
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 26 2010 - 07:30:03 PST
