Thanks Jason, I created the frcmod file and the OFF file. But couldnt
figure out how to generate the prep file using tleap and the OFF file.
Could you help?
Thanks
On Wed, Mar 26, 2014 at 5:46 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Quoting Jason Swails <jason.swails.gmail.com>:
>
> >> > 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.)
>
> Yes Jason - I have overlooked the email... regards, Francois
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 31 2014 - 07:00:03 PDT
