From: Jim Parker (
Date: Fri Apr 04 2014 - 14:32:24 CDT

   I guess my concern is the "contaminating secondary interactions". The
porphyrin core is key to the simulations I'm going to be running. The
large aromatic ring structure shares electrons in a non-trivial manner, and
I thought the point of re-parameterizing was to accurately estimate the
partial charges and bond/torsion strengths that were generated by these
secondary interactions. Or am I overanalyzing this system?

I did look at the heme molecule, but the inclusion of an iron atom at the
core compared to my metal-free (free-base) porphyrin, should significantly
affect the partial charges as well as bond strengths.

The only atom that ffTK didn't find a good geometry for water placement was
the hydrogen bonded to nitrogen at the core. I suppose it would not be to
terrible to use the pyrrolidine molecule (I have the parameters as part of
the tutorial exercise) to get the hydrogen parameters. The others I will
use the Gaussian log files generated by ffTK for the full molecule.

>From your post, I would expect that this is reasonable approach.


On Fri, Apr 4, 2014 at 11:08 AM, Mayne, Christopher G

> Jim,
> ffTK positions water molecules using a geometry-based algorithm that takes
> into account the interaction site and atoms bonded to the interaction site
> atom. As you are seeing in your case, it is susceptible to secondary
> interactions for larger molecules, or molecules with complex 3D (i.e.
> non-planar) topologies. In these cases, the user may need to manually
> manipulate the .gau input file to resolve any secondary interactions, which
> is why we include the "Load GAU Files" button for users to visually inspect
> their Gaussian input prior to attempting the optimization calculation.
> For the porphyrin case you present here, I don't believe that there is an
> optimal solution within the context of the cyclic structure. Our
> suggestion, in accordance with CHARMM and CGenFF protocols, would be to try
> fragment your larger structure into smaller, simpler structures,
> parameterize the fragments, and reconstitute your larger molecule from the
> fragments. There are several reasons for this suggestion; in addition to
> reducing contaminating secondary interactions, fragmentation reduces heavy
> atom counts, which is essential for some of the high level QM calculations.
> You should also take a look at the toppar_all36_prot_heme.str file in the
> stream folder of the CHARMM36 distribution (available from Alex MacKerell's
> website) to see if you can use them as-is, or with minor refinements using
> ffTK.
> Regards,
> Christopher Mayne
> On Apr 4, 2014, at 5:42 AM, Jim Parker wrote:
> > Hello,
> > I am attempting to use ffTK to parameterize a porphyrin molecule. All
> works well until I attempt to find the water interaction energy between a
> water molecule and the hydrogen on the interior pyrrole units (attached
> .pdb with molecule).
> > The problem is that the line of interaction defined by the ffTK
> program causes the water to be too close to the hydrogen on the other side
> of the ring (.gau file attached also). I could arbitrarily rotate the line
> out of the plane of the molecule, which would "fix" the "atoms too close"
> error in Gaussian, but I don't know what was the guiding principle for
> choosing the original line. It appears to be the direction of closest
> approach to the molecule from "outside", but how critical the charges rely
> upon that line I don't know.
> > Bottomline, I can't run as is. What guidance can you give for
> updating the .gau file?
> >
> > I'm using VMD version 1.9.2a35
> > And have found the screencasts very helpful, but don't address this
> issue.
> >
> > BTW,
> > ffTk is a very helpful tool, thanks for your work on this.
> >
> > Cheers,
> > --Jim
> > <TPP-opt.pdb><PORF-DON-HA.gau>