Closed supernova4869 closed 3 years ago
It's not clear whether it's because the molecule is too large (with 25 heavy atoms I would instead recommend you work with smaller fragments), or whether something else is happening. Are you able to coarse-grain small test molecules? See Readme file for instance.
I tried to martinize coumarin 6 molecule (containing 25 atoms) with auto_martini. However, the program output the following information:
and did not output the CG structure and topology of my molecule.
My command:
python auto_martini --smi "O=C1C(C2=NC(C=CC=C3)=C3S2)=Cc4c(O1)cc(N(CC)CC)cc4" --mol COU --cg COU_CG.gro --aa COU_AA.gro -v
The molecular structure of coumarin 6 was at
I used auto_martini with Python 2.7 in Anaconda 3, on Windows 10 operating system.