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

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 4 09:49:38 PDT 2019

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.

> 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. 

More information about the Chimera-users mailing list