VMD-L Mailing List

From: Aaron Larsen (alarsen_at_molbio.mgh.harvard.edu)
Date: Thu Jun 18 2015 - 14:27:55 CDT

Hi Christopher,

I've measured the deflection of the amino group from a planar geometry and
it seems that it's somewhat intermediate between trigonal planar and
tetrahedral, which might be a reasonable expectation. I have not compared
it statistically to a well parameterized amino-containing nucleobase,
however. I have begun paying special attention to the angle and dihedral
force constants for the other ring bonds and I believe that if I find cause
to strengthen these associations, it may help 'calm down' the aminos. I'll
let you know if I make any more progress.

Best,
Aaron

On Thu, Jun 18, 2015 at 2:26 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Aaron,
>
> I'm cc'ing VMD-L so that others can benefit from our discussion.
>
> One of my colleagues in our labs has observed this behavior with a
> molecule that looks similar to guanine. I have tested the geometry
> optimization setup using ffTK for aniline, 1-naphthylamine, and a
> substructure of our guanine-like molecule, and I cannot reproduce the
> distortion towards tetrahedral character for exocyclic amines conjugated to
> the aromatic system.
>
> Have you made any progress on these molecules?
>
> Regards,
> Christopher Mayne
>
> On Jun 12, 2015, at 10:48 AM, Aaron Larsen wrote:
>
> Hi Christopher,
>
> Of course. The nucleobase geometry before the opt. geometry step was
> totally planar with respect to the aminos, exactly as you would expect. The
> output from Gaussian featured the same aminos but now with tetrahedral
> geometry with respect to the aminos. I corrected the geometry manually in
> the resulting pdb files, hoping that would be sufficient to continue.
> However, when I run simulations with the fully parameterized molecule, I
> continue to see the amino groups adopt a tetrahedral geometry. In fact, the
> heterocycles seem to distort slightly from a planar geometry overall. This
> indicates to me that perhaps the torsions or angle force constants are too
> low.
>
> Any advice on how to correct this issue would be most appreciated.
>
> Best,
> Aaron
>
> On Fri, Jun 12, 2015 at 11:18 AM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> Aaron,
>>
>> I'm not sure what you mean by:
>> > FFTK seems intent on treating these aminos as tetrahedral in geometry
>>
>>
>> Can you expand on where the perceived problems with geometry are
>> occurring?
>>
>> Regards,
>> Christopher Mayne
>>
>>
>> On Jun 12, 2015, at 8:03 AM, Aaron Larsen wrote:
>>
>> > Hello VMD users,
>> >
>> >
>> > I'm in the middle of parameterizing a bunch of nucleobase like
>> molecules with the FFTK. Some of them are decorated with aminos. These
>> amino groups SHOULD be planar in geometry, reflecting the aromatic nature
>> of the heterocycles to which they are attached. However, FFTK seems intent
>> on treating these aminos as tetrahedral in geometry. It seems that there
>> should be a simple work around for this. Would anyone have any suggestions
>> on how to proceed?
>> >
>> > It would be preferable if the solution did not involve starting over
>> from the Molefacture step.
>> >
>> > Best,
>> > Aaron
>>
>>
>
>
> --
> Aaron Larsen, Ph.D.
> Harvard University Department of Chemistry and Chemical Biology
> Harvard Medical School Department of Genetics
> E-mail: alarsen_at_molbio.mgh.harvard.edu
> Mobile: 617-319-3782
> FAX: 617-643-3328
>
>
> 

-- 
Aaron Larsen, Ph.D.
Harvard University Department of Chemistry and Chemical Biology
Harvard Medical School Department of Genetics
E-mail: alarsen_at_molbio.mgh.harvard.edu
Mobile: 617-319-3782
FAX: 617-643-3328