thank you all,
This was exactly what I was looking for. I had no real idea of what people had tried/used to date, so this is very helpful.
The specific system I'm using is ilMM. I'm still learning about many of the internal tradeoffs and assumptions that each system is making, but these are great tips and should get me started.
Thanks!
-denny-
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Alan
Sent: Sunday, March 28, 2010 4:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] transforming Antechamber GAFF parameters into another force field
My 2 pence Denny,
I've developed ACPYPI (acpypi.googlecode.com) and in some way I started it
because I had the questions you have. I don't know ENCAD but I know OPLSAA,
Amber ff, gromos and a bit of Engh & Huber used in CNS/XPLOR.
Although ACPYPI doesn't do the full conversion for OPLS, my experimental
approach is not that great, I would know a way using MKTOP to achieve that,
but first I would need time to convert this perl code to python. And here I
think we converge in our quest.
The idea behind acpypi is that we have an API that read all the info
possible from a prmtop file from Amber and put this in a "object". And you
know well what you want, you can "play" whit this object to generated the
topology and parameters in the format you want.
There's also topolbuild 1.3 done by Bruce Ray who used antechamber libs to
generated force filed parameters for different force fields, albeit for
Gromacs format. He claims you can build a dictionary for you aimed ff and so
use his engine to generate the top and par, again, in gmx format.
What I want to say in the end is in some way converging to what Gustavo
said. You can study antechamber and devise a solution for you case.
Essentially, I found out (as others have done as well, e.g. Bruce Ray and
Elmar Krieger for YASARA Autosmiles, he uses Yamber and Amber ff) that the
topology builder code in antechamber is simply the best. What you need if
you want to adapt this to another force fields is:
1) to know if the target FF is "compatible", i.e. e.g., improper dih in
amber ff (for which antechamber was designed) need to be adapted as proper
dihedrals if you're using Gromacs MD engine (see ffAMBER project). In this
sense OPLS is truly compatible.
Essentially, the tools in antechamber can be used to generate the
topology per se, i.e., atomtypes, bonds, angles and proper dih and imp dih
(but pay attention, there's no out-of-plane imp dih in amber ff or opls as
in e.g. gromos96).
2) develop you own mechanism to find out and apply the parameters (the
values for bonds, angles, vdw etc.) to your bonded and non-bonded
parameters. I don't know how licit would be to use the am1-bcc charges (I
don't know how encad determine them), but I would assume it's ok.
Well, those are roughly ideas but it's what I and others seemed to have
done.
I hope you know well about encad (why not using amber99sb or gaff?) and if
you interest in knowing more about acpypi, please look at the link above and
contact me in private.
Good luck,
Alan
On Sun, Mar 28, 2010 at 05:30, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> Hi Denny,
>
> Here's an idea, although I've never tested it, so I'm not sure how
> well it could work.
>
> Notice that Antechamber is actually comprised of a series of small
> programs, that are called in sequence by a main routine and that can
> be used to create job files for QM programs, read the QM results,
> calculate charges based on various models, etc. But nothing prevents
> you to call the programs directly. So, I suppose you could check the
> parameterization procedure for **your** force field, and try to write
> a script that will call the antechamber programs with the appropriate
> flags then treat the results to generate parameters for the force
> field you want.
>
> Probably not the solution you wanted, but it's all I got for now :-)
>
> Good luck,
> Gustavo.
>
>
> On Fri, Mar 26, 2010 at 7:00 PM, Denny Bromley wrote:
> > Hi All,
> >
> >
> >
> > 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?
> >
> >
> >
> > Thanks!
> >
> > -denny-
> >
> >
> >
> >
> >
> >
> >
> > p.s. I apologize if this has been covered already. I searched the
> archives
> > but never really found any search terms that worked...
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Mon Mar 29 2010 - 10:00:03 PDT
