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I have a protein with a nonstandard substrate validol and guanosine di phosphate. I am using CHARMM36-2021 ff along with a cgenff .str that was modified according to the protein-ligand tuitorial by justin Lemkul and subjected to the charm2gmx script to produce .itp file and a prm. The script commented that I need to " Additional parameters needed by the molecule are written to va7p.prm, which needs to be included in the system .top"
I did not add the prm and ran into issues running grompp for assembling a ions.tpr to begin energy min.
ERROR 1 [file va7p.itp, line 248]:
No default Proper Dih. types
ERROR 6 [file gdpv.itp, line 309]:
No default U-B types
ERROR 41 [file va7p.itp, line 5]:
moleculetype VA7P is redefined
I want clarification that my applying the .prm to the bondedd.ff of my charm36ff will resolve the " No default Proper Dih. types" error and in line 5 of my va7p is just the molecule name VA7P. is it the change in letter case thats causing a problem?
Could you please help me to solve this??
Thanks, in advance.