VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Mon Nov 19 2012 - 19:19:23 CST

Yeah, "fortunately" my job failed to get properly assigned to nodes for unrelated issues so I managed to catch this problem before any actual calculations started. While, that script probably provides a quick and dirty solution... I found it much easier to just import the structure into another program. I have a hard time believing that this is really how the tool in VMD works and still think I must be missing something. I've never used VMD to look at QM outputs or generate inputs before - but with all the atom selection and manipulation tools already build in I feel it could be a great QM interface. It could be super slick for setting up ONIOM calculations. If it could render orbitals and display partial charges and whatnot, it would be better than GuassView... of course I guess what I'm really describing is GaussView with a better interface and is likely a lot of work for the developers thats beyond the scope of what the aim of VMD is.

-Erik
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Bennion, Brian [Bennion1_at_llnl.gov]
Sent: Monday, November 19, 2012 2:51 PM
To: Mayne, Christopher G
Cc: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: VMD QMTool. .

I had a similar gotcha with a carbon labeled CA.
Half way through the opt job I noticed the whole molecule flying apart because gaussian was actually using calcium atom.

Brian

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Mayne, Christopher G [cmayne2_at_illinois.edu]
Sent: Monday, November 19, 2012 11:20 AM
To: Martin, Erik W
Cc: vmd
Subject: Re: vmd-l: VMD QMTool

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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