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
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Received on Wed Mar 26 2014 - 05:30:02 PDT
