GROMACS version: 5.1.2
GROMACS modification:No
Force Field used: CHARMM36m-2018-nov
I’m trying to simulate polypeptides containing D amino acids. I generated the pdb files using molefacture plugin of vmd and changing the residue name, for example ALA to DALA in the pdb file.
But after generating the topology file using pdb2gmx, the residue name was still ALA instead of DALA in both the .top and the .gro files generated.
I tried manually modifying the top and gro files by replacing the residue names, but the D-Amino Acid was categorized as “Others” and not “Protein”.
Please help me troubleshoot this issue and suggest a method to simulate D-Amino Acids using Gromacs and CHARMM force field.
If the input coordinate file (presumably PDB format?) was correctly formatted, the residue names should have been preserved. Are the atom types assigned correctly; that is, are Cα atoms type CTD1 and not CT1?
This is intrinsic to GROMACS, which recommends certain residues as Protein, DNA, RNA, etc. Nonstandard residues (like D-amino acids) will not be categorized as standard protein groups. It has no functional implication for the simulation, merely the convenience of referencing groups. You can create an index group for the protein and name it Protein if you need.
Hi Dr. Lemkul.
The system I’m simulating is L_GLY-D_ILE-L_GLY tripeptide. The pdb file is:
But the .gro and .top files generated by pdb2gmx still had name ILE instead of DILE for D-Isoleucine, and also the C α atom was CT1 instead of CTD1.
I tried to manually change the labels from ILE → DILE and CT1 to CTD1 in both the .gro and .pep files, but got an error in the grompp step I performed later.
No default Proper Dih. types ,No default U-B types,No default Bond types.
Is this error due to the .pdb file. Should I use some other molecule editor (TLEAP maybe, instead of molefacture) to generate the tripeptide .pdb ?
Ash
This is because your PDB file is incorrectly formatted. the “D” in “DILE” is ignored because it is one character too far to the left.
The missing parameter problem will be solved by using a more recent version of the CHARMM36 port. We didn’t have parameters for mixed D/L peptides back in 2018, but we do now.