On Wed, Apr 04, 2012, kanika sharma wrote:
>
> I used distance dependent dielectric constant flag to minimize a protein
> using the script in implicit solvent :
>
> initial minimisation prior to MD
>
> &cntrl
> ntpr = 10,
> ntb = 0,
> igb = 1,
> dielc = 4,
> cut = 12,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc =1000,
> ncyc=500
> &end
>
> &ewald
> eedmeth=5,
> &end
You can't use distance dependent dielectric *and* igb in the same run.
When you set igb=1, it selects a code path that never sees or uses the
eedmeth=5 option.
Are you sure you want to use a distance-dependent dielectric? I'm not sure
we should even offer such an option anymore. Consider using GB instead:
use the default dielc, and consider using igb 7 or 8 for proteins.
...dac
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Received on Wed Apr 04 2012 - 06:30:04 PDT
