the manuscript on these is under review. I think Jason's script is ready.
mbondi2 radii are ok but mbondi3 are optimized and do indeed give much
improved salt bridge strength and other properties.
On Tue, Sep 6, 2011 at 1:56 PM, Peter Varnai <P.Varnai.sussex.ac.uk> wrote:
> Dear All,
>
> This is to inquire whether there has been any update regarding the mbondi3
> parameters for protein simulations with igb=8.
>
> The amber11 manual states (p. 57) that the mbondi2 radii are fine to use
> with igb=8 which Carlos mentioned is the case indeed on 27 April but some
> new modifications are available to improve those results for salt bridges.
> The manual also details new scaling and atom-specific parameters which all
> seems to have been implemented in mdread.f (apparently these can be changed
> in the mdin file).
>
> I would be happy to update the protein atom radii in the prmtop file to the
> most recent mbondi3 values: (i) has the paper been published that gives
> those values? (ii) Jason's python script may be made available that corrects
> for those? (iii) is there a leap fix available?
>
> Many thanks,
> Peter
> _______________________________________________
> 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 Sep 06 2011 - 12:00:03 PDT
