From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Oct 01 2011 - 08:31:05 CDT

On Sat, 2011-10-01 at 17:47 +0530, lara lara wrote:
> Dear users !
>
> I have read the solvate plugin
>
> it mention to create the following files
> -------
>
> An equilibrated, cubic box of the solvent of choice (-spdb)
> A psf file for the solvent cube (-spsf)
> A topology file for all residue types in the solvent (-stop)
> A key selection which will occur once in each solvent residue (eg.,
> "name OH2") (-ks)
> The side length of the box (should be taken from the equilibration's
> periodic cell (-ts)
>
> -------
>
> so , how to create these files for methanol ,
>
> if any one can explain me in detail it will be useful.

the "in detail" part won't happen. most of what you have
to do is standard MD protocol with some minor changes, and
you can easily teach that yourself. if you want to use a
non-standard solvent, you better know what you are doing.

most of the techniques and details that you need to know
about are described in the psfgen/topology tutorial. you
just need to apply some common sense to translate the
examples to your specific case.

if you get stuck at any point, you are most welcome to
ask specific questions about individual details, however
that bulk of the questions you may encounter you can
answer by yourself from the available tutorials,
documentation, and literature. it will be good practice.

good luck,
     axel.

>
>
> On Sat, Oct 1, 2011 at 5:38 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> On Oct 1, 2011, at 7:45 AM, lara lara <lara.4884_at_gmail.com>
> wrote:
>
> > Dear Users !
> >
> > I would like to put the methanol box for my peptide
> >
> > can any one suggest me how to solve this
>
>
> Use the solvate plugin.
>
> Axel.
>
> >
> > thanks in advance
> >
>