Re: [AMBER] Se atom type

From: Jason Swails <>
Date: Sat, 21 Jun 2014 23:16:18 -0400

> On Jun 21, 2014, at 8:37 AM, Krisztina Feher <> wrote:
> 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
> help.
> Thanks,
> Krisztina
> 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...

I won't be of much help unfortunately. Your first email came through, but I didn't answer because I have no experience (at all) with selenium parameterization. On one hand, you can see if anybody has worked with those compounds using a different force field. In many cases , bond and angle equilibrium values and force constants are transferable, but other terms like partial charges and torsion potentials are not. (Of course this should always be checked). Otherwise if nobody else has worked with selenium compounds that answers questions here, you may be on your own as far as determining the parameter sets for it. But we can probably help with some of the individual steps in the parameterization process if you get stuck.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Jun 21 2014 - 20:30:02 PDT
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