home/eduardo/bilayer/cg-to-aa/backward.py initram-v5.sh -f o -p topol.top -po backmapped.top -o o -from martini -to gromos54a7īackward.py. Here is the output of the failed initram-v5.sh execution: If anyone knows what I'm doing wrong I would appreciate the advice.
The problem then arises when the scripts tries to execute the grompp for performing energy minimization, once topology and coordinate files doesn't have the same amount of atoms. The o generated in the first step misses all of the dppc molecules while the backmapped.top has, as expected, the 128 dppc molecules. When I execute initram-v5.sh something weird happens. I built the atomistic target topology using a extended version of the gromos54a7 force field that includes parameters for lipids.
Now I'm having problems in backmapping the system to all atom. A build the system with the dppc molecules placed randomly in the box and performed a 30 ns simulation with martini force field. My system is composed of a protein dimer (each domain with 131 residues) and 128 dppc molecules with water as solvent.
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