Hello,
I would like some guidance on how to handle terminal capping groups when using the AMBER force field in GROMACS. The .rtp file appears to include only ACE and NME, and the -ter option is not available with AMBER. What would be the recommended approach for adding alternative caps in this case?
Additionally, AMBER documentation indicates support for D-amino acids, but there are no corresponding entries in the .rtp file. How should these be incorporated into a GROMACS workflow?
It’s been a long time since I tested this but this workflow could help you, particularly in the D-aa case:
This is only handling the structural part though - you should be able to copy ACE and NME into your D-aa .rtp and use it almost as-is.
If you’re adding other capping groups, you need to verify that (1) residuetypes.dat lists them as “Protein”, (2) the new .rtp entry has compatible “incoming” and “outgoing” atoms included (like the “-C N” bond to the previous residue in NME), and (3) the .hdb adds the hydrogen atoms correctly.