Re: [AMBER] mbondi3

From: Mike NG <>
Date: Sat, 28 Apr 2012 14:07:07 -0400

You can specify 'mbondi3' in tleap of amber12.


On Tue, Sep 6, 2011 at 1:56 PM, Peter Varnai <> 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
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Received on Sat Apr 28 2012 - 11:30:03 PDT
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