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

From: bio lab <>
Date: Fri, 19 Oct 2012 02:05:47 +0200

> 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.
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Received on Thu Oct 18 2012 - 17:30:10 PDT
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