On Wed, Mar 26, 2014 at 3:24 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear DEBOSTUTI GHOSHDASTIDAR,
>
> > Could anyone suggest if there is a way to generate frc and prep files for
> > an organic molecule, say X, from the topology file of a system containing
> > large number of X in a box of water? It would be kind of going backward.
>
> Here you need to read a little bit; i.e. the Amber manuals and perform
> a google search...
>
> In short use Antechamber from the AmberTools or R.E.D. Server
> Dev./R.E.D. Python at q4md-forcefieldtools.org.
>
Unless I'm mistaken, R.E.D. (and definitely antechamber) are designed to
go 'forward', that is when you want to parametrize a new organic molecule
in order to _create_ a topology file.
If you already have said topology file (as I believe the OP said he did),
and you want to extract a library (mol2, OFF, or prep) file as well as an
frcmod from the information already present in the topology file, I believe
that ParmEd is your only option for doing so. (That said, ParmEd can only
create a OFF file, not a mol2 or prep; but that OFF file is sufficient for
tleap which you can use to create a mol2 or prep.)
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 26 2014 - 03:30:02 PDT
