Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information related to the DPPC lipids as reported in the manual? I mean: is it ok if I use the topology file created at the beginning from pdb2gmx command on the protein and modify it? thanks.
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