Thanks Nicholas, I can clarify. Sorry for any vagueness. :)
My big question is this: I need to parameterize a bunch of small molecules
to dock against proteins that are already parameterized in another force
field. Parameterizing the small molecules by hand using GAMESS or something
is not really feasible. So, Antechamber sounds great except that it's using
a different (albeit similar - ENCAD) force field. So I want to take what
Antechamber gives me and transform it into something that will work in our
force field.
Like I said, I have some ideas, but if there is a well-known method for
transforming parameters between force fields, I would love to hear about it
before I invest a ton of time in this.
thanks for your help-
-denny-
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Nicholas Musolino
Sent: Friday, March 26, 2010 3:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] transforming Antechamber GAFF parameters into another
force field
Dear Denny,
It seems like there are two questions you're asking: (1) is it possible to
perform GAFF parameterization in an automated fashion? And (2) is it
possible to convert GAFF parameters to some other force field?
To answer question (1), I have been able to successfully employ GAFF in an
automated fashion, provided that the inputs to it aren't too bad. By that I
mean, I supply antechamber with MOL2 files with atomtype and topology
already established, and with reasonable structures. I found that when
supplying PDBs and asking Antechamber to do atomtype perception, bondtype
perception, and parameter assignment, it was too much work for antechamber
to do reliably over hundreds of molecules.
In practical terms, to automate this process, you could use a shell (BASH)
script, and program the script to do whatever you would do by hand for an
individual case.
To answer question (2), it's not immediately clear what you want to do. Are
you saying that you want to use the GAFF parameters alone in a simulation
(e.g. a pure liquid of some novel molecule)? Or that you want to transform
the GAFF parameters to work with some other FF? Remember, mixing and
matching force fields in one simulation (or in one study of a molecule) is,
generally speaking, not a good idea.
Don't forget that you can use the AMBER force field and appropriately
formatted PARM7 files with other MD packages, such as NAMD. See
http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node14.html
Hope this is helpful!
Nicholas Musolino
---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino.mit.edu | 617-253-6675 | Room E19-528
On Mar 26, 2010, at 6:00 PM, Denny Bromley wrote:
>
> I need to parameterize 100-200 small molecules into our force field and
> would like to avoid doing it all from scratch. Antechamber would be
perfect
> except that we aren't using Amber (or GAFF). However, it does provide
> parameters for a self-coherent molecule, so I feel like I'm almost there
if
> I can just find a transform. I've got some ideas, but I don't really want
> to re-invent the wheel, particularly if they've been shown to not work.
> Have there been any successful efforts in this direction so far?
>
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Received on Fri Mar 26 2010 - 16:30:04 PDT
