From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Sat Nov 08 2008 - 15:17:44 CST
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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