Re: [apbs-users] circular DNA

[Nathan B. <nat...@gm...>]

Hi Harry --

I apologize for the delayed reply.

These grid settings are a little coarse but otherwise reasonable.  I notice
that you're solving the NPBE with no mobile ions -- is there a particular
reason for this?

You might trying increasing the cglen values to a ~600 A to see if this
improves your results and reduces the error messages.  APBS is complaining
about large potential values during the focusing operations since it raises
the possibility that the calculations may not converge.

Thanks,

Nathan



On Tue, Dec 1, 2015 at 1:40 AM, Harry Mark Greenblatt <
har...@we...> wrote:

> BS”D
>
> Dear Nathan,
>
>    Thanks for your reply.  I simply used the default settings (except for
> the use of the non-linear form), as below.  If you want I can send you the
> coordinates off-list.
>
>
> Harry
>
>
> read
>     mol pqr 14489618082.pqr
> end
> elec
>     mg-auto
>     dime 513 65 513
>     cglen 403.446 39.9014 405.284
>     fglen 257.321 39.9014 258.402
>     cgcent mol 1
>     fgcent mol 1
>     mol 1
>     npbe
>     bcfl sdh
>     pdie 2
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     sdens 10
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     calcenergy total
>     calcforce no
>     write pot dx 14489618082-pot
> end
> quit
>
>
>
>
> On Nov 29, 2015, at 7:29 PM, Baker, Nathan <Nat...@pn...> wrote:
>
> Hi Harry --
>
> We'll need more information in order to help you.  Can you provide the
> input file settings that you used?
>
> Thanks,
>
> --
> Nathan Baker
> Computational and Statistical Analytics Division — Pacific Northwest Natl
> Lab
> Division of Applied Mathematics — Brown University
> +1-509-375-3997 — http://www.dam.brown.edu/people/baker/
>
>
> --------------------------------------------------------------------
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           har...@we...
> Weizmann Institute of Science        Phone:  972-8-934-3625, -6340
> 234 Herzl St.                        Facsimile:   972-8-934-4159
> Rehovot, 7610001
> Israel
>
>
>
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