[AMBER] Se atom type

From: Krisztina Feher <feher_krisztina.yahoo.com>
Date: Sat, 21 Jun 2014 05:37:34 -0700

Dear All,

I would like to simulate a peptide with diselenium bonds. I would be
reluctant to use sulphur instead, because, unlike Se-methionines used in X-ray studies, 4 diselenium bonds in an oligopeptide should result in a different enough structure and dynamics compared to the disulphide
analogue to justify using a Se atom type. However, I did not seem to
find Se in the AMBER14 force fields. Although Se has been discussed
several occasions on the AMBER list, I also did not find specific
parameters to make a new Se atom type. I have found Lennard Jones parameters in this paper (attached): 
An interatomic pair
potential for cadmium selenide Eran Rabani J. Chem. Phys., Vol.
116, No. 1, 1, 2002
If anyone have experience with Se, I would very much appreciate any

p.s. Sorry if this mail appeared twice, so far it looked like it has not been distributed to the list due to bounces, which disabled my membership...
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Received on Sat Jun 21 2014 - 06:00:02 PDT
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