I'm trying to generate a .itp and .gro file with simple tri-peptides with an electrophilic warhead attached
Actual Behavior
When the warhead contains an enone motif, The output file has carbon atoms completely out of place (usualy the CH3 on motif R-O-CO-CH-CH-CH3 )
I've tried different ways of generating my .mol file and inputing the SMILES code, but it doesn't work.
Issue Information
Software name & Version : Gromacs 2018.7 Method:
Expected Behavior
I'm trying to generate a .itp and .gro file with simple tri-peptides with an electrophilic warhead attached
Actual Behavior
When the warhead contains an enone motif, The output file has carbon atoms completely out of place (usualy the CH3 on motif R-O-CO-CH-CH-CH3 ) I've tried different ways of generating my .mol file and inputing the SMILES code, but it doesn't work.