But now I did have all the crystal lattice parameters and space group, still solve it using first step?
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: jun kit <klorin2002.yahoo.co.uk>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 19 September 2011, 12:00
Subject: Re: [AMBER] force field of molecular crystals
On Mon, Sep 19, 2011, jun kit wrote:
>
> In order to generate a force field and topology for a molecular crystals
> (which already in pdb file), and my crystal do not involve any solvent,
> just solid crystals, which proper steps should I follow:
You should run antechamber on single, individual, relatively small,
closed-shell organic molecules. So item 1 below sounds closest, given that we
don't know what is in each unit cell.
>
> 1. Run antechamber on the "free" crystal structure finding resp charges
> fitting the gaff. Then only run UnitCell and PropPDB. Then run tleap for
> creating prmtop and inpcrd file.
>
>
> p/s: i want to find phase transition,
!!! Generally speaking, finding phase transitions is a super-hard problem.
Be sure to look for literature where similar problems were faced (and solved);
it is likely to involve simulations that are far from "standard" ones.
....dac
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Received on Mon Sep 19 2011 - 12:30:03 PDT
