Re: ffTK Without Using Gaussian

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Tue Mar 20 2018 - 12:59:34 CDT

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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