Re: [AMBER] Se atom type

From: Krisztina Feher <>
Date: Mon, 23 Jun 2014 04:43:35 -0700

Thanks, Jason!Good to know that my mails are distributed to the list again. I got already the third message that my membership was disabled due to bounces. Any idea why that should happen with a address, which I regularly use?

As for selenium I have found that people used parametersfrom UFF in GROMACSor from CVFF in Insight II. Strangely, I did not see Se implementedin CVFF in InsightII. As for UFF in GROMACS, there is a webserver called OBGMX (, which is generating parameters and topologies for Se too, but I still have to dig into the details. In the meantime I will analyse MDs on the disulphide variants, maybe I already get some answers for the dynamic behaviour observed with Se77 NMR.

Thanks again,

 From: Jason Swails <>
To: Krisztina Feher <>; AMBER Mailing List <>
Sent: Sunday, June 22, 2014 5:16 AM
Subject: Re: [AMBER] Se atom type

> 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
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Received on Mon Jun 23 2014 - 05:00:03 PDT
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