[Chimera-users] PDB file of D-amino acids

[Elaine Meng]

Hi Mohsen,
If you are asking in general, it may be beyond the scope of this mailing list.  You would have to investigate further into CHARMM or whatever software/forcefield combination you are using for molecular mechanics/dynamics.

I  would guess the answer is “not necessarily” because some force fields or programs may apply chirality restraints — you might have to use different residue names and different parameter files for D-amino acids than for their L- counterparts. 

If you mean in Chimera, doing minimization/MD using MMTK (which does not have any CHARMM forcefield options), I don’t know how well it would work, but you could try.   If you do, would need to check results carefully for any strange distortions.
Regards,
Elaine

> On Apr 4, 2019, at 5:32 AM, Mohsen Asadbegi <mohsenasad.7091 at gmail.com> wrote:
> 
> Thank you for the precise clarification,
> 
> Regarding Force field, does it possible to use the existing force fields of L-amino acids (For instance CHARMM36) for D-amino acids?
> 
> Regards, 
> Mohsen.