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> wrote:
> On Thu, Oct 8, 2015 at 12:41 PM, David A Case <david.case.rutgers.edu>
> 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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Received on Fri Oct 09 2015 - 02:00:03 PDT
