VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Apr 04 2014 - 11:08:13 CDT
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.
On Apr 4, 2014, at 5:42 AM, Jim Parker wrote:
> 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.
> ffTk is a very helpful tool, thanks for your work on this.