Hi, I am simulating a peptide having alternating L and D amino-acid in lipid bilayer (DMPC). So I use the input generator for protein/membrane complex in CHARMM GUI and I run standard mdp files in gromacs.(force field that I have opt for is CHARMM36)
> My aim for simulation is to observe the dihedral angle of each residue in ramachandran plot.
> Error that I am getting-
> My peptide is 14 residue peptide and everything run flawlessly but after extracting the data for dihedral angle and plotting it I can see one D amino acid residue is in second quadrant of ramachandran plot. It's a disallowed region for D amino-acid residue right?
> I am attaching a drive link here in which there is a screenshot of DALA-6 ramachandran plot and there you can see some dihedral angle come in second quadrant and some in 3rd which is not allowed region for D aminoacid.

and in LD14_2_updated folder that i have attached there are all files including initial structure, mdp files that i have generated by charmm gui.

please have a look and do comment if something seems wrong.

I have done the whole simulation in gromacs
> A quick reply would be appreciated

Last edited by Rakesh; 01/18/21 08:41 PM.