Thank you guys. I had the impression that "setBox mol vdw" redefines the
truncated octahedron dimensions to fit to the vdW radii of the outer layer
of atoms. I used it when adding extra atoms/ions with AddToBox program and
left it there. Thanks again and sorry for the confusion.
Thomas
On 31 January 2013 23:26, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Jan 31, 2013 at 2:16 PM, Thomas Evangelidis <tevang3.gmail.com>
> wrote:
> > solvateOct mol TIP4PEWBOX 15.1
> > setBox mol vdw
>
> I think the setBox command is overriding the solvateOct command; you
> can see that the ifbox part of your POINTERS section (3rd from last)
> is '1' instead of '2' (2 is truncated octahedron).
>
> > %FLAG
> > POINTERS
> > %FORMAT(10I8)
> >
> > 129517 19 96235 33109 35154 2084 6961 5382
> > 0 0
> > 238260 31925 33109 2084 5382 50 100 70
> > 35 1
> > 0 0 0 0 0 0 0 1
> > 24 0
>
> The setBox command is not necessary since solvateOct will set up the
> box information necessary for truncated octahedron.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jan 31 2013 - 14:00:03 PST
