[gmx-users] D-amino acids simulation

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 20 16:31:46 CET 2006

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 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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