Hi,
Lists in leap are enclosed by curly braces {}, e.g.
{10 20 10}
Hope this helps,
-Dan
On Friday, October 9, 2015, Nicholus Bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> help solvateBox inside tleap gives the following
>
> "If the buffer argument is a LIST of three NUMBERS, then the NUMBERs are
> applied to the x, y, and z axes respectively. As the larger box is created
> and superimposed on the solute, solvent molecules overlapping the solute
> are removed."
>
>
> so I tried the command
>
> >solvateBox mysolute solvent 10 20 10 1
>
> However, its giving me error with
>
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>
> Am I not doing it in the right way? Shoul I use some kind of parenthesis
> for x,y,z values.
>
> On Thu, Oct 8, 2015 at 6:50 PM, Jason Swails <jason.swails.gmail.com
> <javascript:;>> wrote:
>
> > On Thu, Oct 8, 2015 at 12:41 PM, David A Case <david.case.rutgers.edu
> <javascript:;>>
> > wrote:
> >
> > > On Thu, Oct 08, 2015, Nicholus Bhattacharjee wrote:
> > > >
> > > > So considering helix
> > > > axis to be in the Y direction the box size will be somthing like
> > 32.302 X
> > > > 84.333 X 34.369. Can it be done with the tleap? Thank you for the
> help.
> > >
> > > Yes, LEaP can do this: the "buffer" argument can be a list of three
> > > numbers, which are the buffer values to use in the x,y,z directions.
> > > Inside tleap, type "help solvateBox" to see a much fuller description
> of
> > > this option.
> > >
> >
> > ​Well look at that! I learn something new every day. Sorry for the
> > misinformation (I usually use solvateOct which doesn't have this option
> as
> > far as I can tell), and thanks for the tip.
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
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> >
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Oct 09 2015 - 03:00:03 PDT
