[gmx-users] D-aminoacids in OPLS

[Erik Lindahl]

Hi,

Since OPLS-AA is an all-atom force field the topology will be identical 
for D and L amino acids. As long as you provide correct initial 
coordinates (i.e. D instead of L) the potential barriers between the 
two forms should make sure it stays in D.

Cheers,

Erik

On Mar 16, 2005, at 5:00 PM, Guillem Portella wrote:

>
> Dear users,
>
> I'm currently trying to generate a topology for D-aminoacids, namely 
> D-leucine
> and D-valine, using OPLS force field. In ffgmx this was quite
> straightforward. I know that OPLS does not use improper angles for 
> chiral
> center. I cannot find the angle or group of angles that have to be 
> modified
> (and how...), because the chiral center is not directly involved in 
> this
> definitions. Does anybody have a clue?
>
> This is where this angles are defined, e.g. in L-leucine
>
>  [ dihedrals ] ; override some with residue-specific ones
>      N    CA    CB    CG    dih_LEU_chi1_N_C_C_C  <-- RB Fourier 
> series coeff.
>     CG    CB    CA     C    dih_LEU_chi1_C_C_C_CO
>  [ impropers ]
>     -C    CA     N     H    improper_Z_N_X_Y
>     CA    +N     C     O    improper_O_C_X_Y
>
> where  #define improper_Z_N_X_Y        180.0      4.18400   2
>
> Thank you very much in advanced,
>
> Guillem
>
>
> *******************************************************
>  Guillem Portella
>  Computational biomolecular dynamics group at the
>  Max Planck Institute for Biophysical Chemistry
>  Am Fassberg 11
>  D-37077 Goettingen -- Germany --
>  phone: ++49-551-2012309
>  fax: ++49-551-2012302
>  Email: gportel at gwdg.de
> *******************************************************
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