Re: ffTK Without Using Gaussian

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Mar 20 2018 - 15:35:40 CDT

Out of curiosity, is it possible to use other QM engines, such as ORCA
<https://orcaforum.cec.mpg.de/> or firefly
<http://classic.chem.msu.su/gran/gamess/index.html>?

Best,
Ajasja

On 20 March 2018 at 20:37, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:

> Thanks for the very thorough response Fotis!
>
> I would just add that an institution being banned doesn’t preclude you
> from using it when available at a supercomputing center, for example. I
> think you just have to sign some papers that you won’t compete with
> Gaussian, you won’t help others to compete with them, and that you won’t
> even think about publishing a benchmark.
>
> Best,
> JC
>
> > On Mar 20, 2018, at 1:59 PM, Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr>
> wrote:
> >
> > Hello Alex,
> >
> > Unfortunately, fftk depends heavily on Gaussian, since all required QM
> steps are done with it.
> >
> > However, the vanilla version of CGenFF parametrization and optimization,
> which also utilizes QM, actually uses a CHARMM module (MOLVIB) for some of
> the QM steps rather than Gaussian (CHARMM the MD simulation suite, that is,
> not CHARMM the force field). Note that from version c40 and onwards, CHARMM
> in its non-parallel version ("charmm") is given free of charge. So in
> principle, you could use CHARMM itself for the parametrization, following
> the tutorials in the CGenFF page: http://dogmans.umaryland.edu/~
> kenno/tutorial/
> > The downside, of course, is that you need to become familiar both with
> the CHARMM scripting syntax and with the underlying mechanics of CGenFF and
> CHARMM parametrization (or find someone with expertise to help you). Plus,
> you won't have all those nice, automated perks that fftk offers.
> >
> >
> > Alternatively, you can look to some of the other CHARMM parametrization
> services that are available out there. A really good option is GAAMP (
> http://gaamp.lcrc.anl.gov/ ) which will do some QM optimization for you.
> However, it is not open to the public and you first need to get in contact
> with the team behind it to obtain access.
> >
> > Other, freely available options include MATCH (
> http://brooks.chem.lsa.umich.edu/index.php?matchserver=submit ) and
> SwissParam (http://www.swissparam.ch/ ). However, both have their
> limitations; MATCH does not use QM itself and therefore may also need
> optimization. As for SwissParam, although it performs some optimization,
> it is generally recommended for docking or simple energy calculations
> rather than full MD simulations. Plus, the whole procedure they use
> (mixing the Merck forcefield with CHARMM22) may not be fully compatible
> with CHARMM36.
> >
> > As to whether these QM steps are necessary or not depends, to some
> degree, on how you have set your initial topology/parameters for your
> molecule. Have you made them yourself, using the same procedure as the fftk
> tutorial, or have you gotten them from CGenFF/ParamChem?
> >
> > If the latter applies, first check what penalties CGenFF has assigned to
> the charges and the bonds/angles/dihedrals. If most (preferrably all)
> penalties are low enough (10 or lower are preferred, but if you have 15-20
> it could still be fine), you could just use the initial parameter scheme
> "as-is". If only a few bonded parameters have high penalties, you could
> try fixing them yourself through analogy with other similar molecules, or
> through trial and error (assuming you have anything on your molecule to act
> as reference).
> >
> > If the overall quality of your molecule's parametrization is low, I'm
> afraid you WILL need QM to get meaningful results.
> >
> >
> > Hope I helped,
> > Fotis Baltoumas
> >
> > On 03/20/2018 05:49 PM, Alex Saad-Falcon wrote:
> >> The force-field toolkit uses Gaussian for several of the steps.
> However, my institution is banned from using Gaussian. Can I safely skip
> these steps, or are they necessary? Are there any other ways to
> parameterize a small organic molecule for NAMD?
> >>
> >> Thanks,
> >>
> >> Alex
> >
> > --
> > *******************************************
> > Fotis A. Baltoumas
> > Bioinformatics Postgraduate Programme
> > Section of Cell Biology and Biophysics
> > Department of Biology, National & Kapodistrian University of Athens
> > Panepistimiopolis, Athens 157 01, GREECE
> > --------------------------------------
> >
> > email : fbaltoumas_at_biol.uoa.gr
> > http://biophysics.biol.uoa.gr
> > http://bioinformatics.biol.uoa.gr
> > *******************************************
> >
>
>
>

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