Hi Venkat,
As for your first problem, it is probably the same as this one: Newest CHARMM36 port for GROMACS - #8 by Leonardo. It is a bug in the GROMACS port of the CHARMM36 FF, where the C-terminus entry has been incorrectly constructed. It will be fixed in the next release. Until then, please apply the manual fix in the thread above.
As for your other questions:
- the SAM ligand is implemented in the upstream CHARMM data set (topar_c36_jul21) as a patch residue, which can be applied onto ADE (in the stream file stream/prot/toppar_all36_prot_na_combined.str). As GROMACS does not have such a flexible patching facility, the porting script simply creates the already patched topology in the .rtp file. I’m not sure if CHARMM-GUI can handle patch residues or not, but if you build a molecular model for your ligand (by PyMOL or any 3D chemical builder program) and label the atoms according the topology, you can construct the topology for it by pdb2gmx and combine this and that of your system.
- I’m not an expert in Amber, but if your topology is complete and correct in GROMACS (the topol.top file includes all molecule topologies and the corresponding interaction parameters), then the Amber tools should also make a correct topology.
I hope this helps.
Kind regards,
Andras