Re: ffTK Without Using Gaussian

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Mar 20 2018 - 15:43:43 CDT

This is a relatively recent thread from vmd-l on the subject:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28979.html

On Tue, Mar 20, 2018 at 4:35 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
wrote:

> 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
>> > *******************************************
>> >
>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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