From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun Nov 09 2008 - 15:37:43 CST
The answer to your second question should be (at least implicitly) in
the literature documenting the protein force field, which I recommend
having a look at, if only to realize how happy you are that you don't
work in that area ;-)
Answering question 2) may or may not give you a good answer to
question 1), but at least will tell you whether and how the force
field authors tried to address it... Now if you want my personal
opinion, I would not worry much about this amount of ring bending.
On Sat, Nov 8, 2008 at 5:17 PM, CHINDEA Vlad <vchindea_at_hotmail.com> wrote:
> Dear all
> While doing a small trial MD simulation of a solvated small molecule with
> PBC I have observed that an aromatic ring (indole) is being bent up to 10
> degrees from the planar position. As this is against my chemical common sens
> I took a look in the topology file used (top_all27_prot_lipid_na.inp) and I
> saw that aminoacids with aromatic rings do not have IMPR terms defined for
> the aromatic ring, as I would have expected, but only for the peptide bond.
> My questions would be the following:
> 1. From your previouse experinces is it acceptable to have a 10 degrees
> bending of an aromatic ring ? I know that my simulation was rather short (6
> ps) and that the answer would be dependent on the application, but probably
> there should be also something like a 'rule of thumb' regarding this ?
> 2. How come there are no impropers defined for the aromatic rings in the
> topology files ? Maybe I am missing something but this is what I would have
> expected, considering the definition of these energy terms.
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