Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling

From: Aron Broom <>
Date: Fri, 19 Oct 2012 00:36:08 -0400

actually, I hadn't looked carefully enough at the structure you attached.
I'm somewhat confused now. The cis/trans states are controlled by a
double-bond, so that should mean that the only way to change between them
is for that double-bond to temporarily break no? And that is something you
are not going to be able to do with conventional molecular mechanics, and
will instead need to do some QM stuff on at least that portion of the
molecule. Am I missing something critical here?

So if I haven't lost my mind above, how are you able to see any kind of
change between the forms in your simulation? Unless that isn't treated as
a full double-bond and you modelled it as some kind of peptide-bond like


On Thu, Oct 18, 2012 at 9:30 PM, Aron Broom <> wrote:

> For the RESP server you can do a single conformation as you suggest, and
> hope that the point charges are reasonable for both. I believe you can
> also give multiple structures, in which case something like the average is
> used for the forcefield, but I haven't done that, so can't comment with
> certainty on how it works.
> In terms of the aging. The trans-to-cis kinetics for something like that
> should be really fast (sub-second timescale for sure), as evidenced by the
> fact that you are able to see it at all on your presumably ns long
> timescale MD. So, if the trans conformation is dominant when you make a
> fresh solution and measure it even a minute later, that really strongly
> suggests to me that the trans-conformation is the most stable one for the
> unmodified molecule, and some kind of modification is happening to cause
> the cis-conformation to later become more stable. This is pretty common
> with organic molecules, whether from oxidation of UV light induced
> changes. I'd be extraordinarily shocked if the aging you mention was
> actually just because of a large kinetic barrier between the two
> conformers. I guess that's just my opinion.
> ~Aron
> On Thu, Oct 18, 2012 at 8:05 PM, bio lab <> wrote:
>> > the Guassian methods employed by RESP will allow for accurate
>> > partial charge distribution as a result of the two rings being nearby
>> Ok, I will do it.
>> Please notice that I am interpreting your quoted text as "will give
>> accurate charges as a result of the two rings being nearby in any of the
>> two conformers", not "being nearby in the cis form".
>> In other words, I am modeling the molecule in the trans form, and then
>> assigning the charges to this conformation. And I am assuming that I would
>> obtain equal (or very similar) charges in the case I use the cis
>> conformation as the structure to assign the charges to.
>> Because if the two situations lead to quite different charges, then I
>> would
>> be in trouble, as I cannot obviously modify the charges during the MD
>> simulation. ...Anyway, I will test it too.
>> > what this tells me is that the trans-form of the molecule is more stable
>> > as your MD suggests, and it is some kind of modification to the molecule
>> > (likely oxidation) that changes the structure
>> No, there is no chemical modification of the molecule reported in
>> literature, AFAIK. The cis and trans form are conformational rotamers,
>> just
>> like in the Wikipedia figure in my original post.
>> Thanks a lot for your help.
>> _______________________________________________
>> AMBER mailing list
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Thu Oct 18 2012 - 22:00:02 PDT
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