[gmx-users] D-amino acids simulation

[David van der Spoel]

Arnold Perez Goicochea wrote:
> Dear All,
>
> I am planning to perform MD simulations with some D-amino acids. I 
> normally use OPLS-AA with GROMACS 3.2.1, but I think it won't work if 
> D-amino acids  are used. The FF torsion potential would not be 
> suitable for those aminoacids.
>
Why not?

we have done so already in:
Alexandra Patriksson, Christopher Adams, Frank Kjeldsen, Johan Raber,
David van der Spoel and Roman A. Zubarev: /Prediction of N-Ca Bond
Cleavage Frequencies in Electron Capture Dissociation of Trp-cage
Dications by Force-field Molecular Dynamics Simulations/ Int. J. Mass
Spectrom. *248* pp. 124-135 (*2006*)
> Should I use the OPLS with D-amino acids? or would be better to use 
> another force field?, or in the case no FF is suitable, which kind of 
> modifications should I do on it??
You only need a different conformation as far as I'm concerned.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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