VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Nov 19 2012 - 13:20:06 CST

That's annoying.

I suspect that it's actually using atom names, and not atom types to build the Gaussian input file. A quick way around this is to rename your atoms in a Gaussian-acceptable manner. If the element field is properly filled out in your PDB file (I'm assuming that's how you're brining the coordinates into QMtool), you can rather easily rename all of your atoms using some quick scripting.

from the tkcon:

mol new <pdbfile>
for {set i 0} {$i < [molinfo top get numatoms]} {incr i} {
    set sel [atomselect top "index $i"]
    $sel set name "[$sel get element]${i}"
    $sel delete
}
[atomselect top all] writepdb <reformatted_pdb>

This just serves to rename your atoms with the element followed by the index, which provides a unique element-related identifier for Gaussian.

Then in QMtool load the reformatted_pdb and try to write the Gaussian file.

It ain't pretty, but it should work.

Chris

On Nov 19, 2012, at 11:42 AM, Martin, Erik W wrote:

>
> I tried to use this tool to write a g09 input file from parts of a structure I'd previously used in a namd simulation. I noticed that in the atom types it uses the MD naming convention - which isn't so much compatible with gaussian. For example, hydrogens of the type HG get interpreted by guassian as mercury. I can't find in the gui somewhere I can specify it to use the appropriate atom names. Am I missing something?
>
> Thanks a lot,
> Erik
>
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