Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the "KALP15 in DPPCI" Tutorial and, so far, I managed to obtain my protein (in pdb code) very close to the membrane surface by using editconf and cat command. At this point, I don't know how to get on. 1)How should I generate the topology file which includes the coordinates both of the protein and of the membrane? 2)Furthermore, the lipid molecules are listed in my pdb file with the abbreviation "DPP", whereas I see that those ones are called "DPPC" in the Tutorial. Therefore, Should I replace "DPP" abbreviation with "DPPC" in my pdb file? Could this difference cause any bugs in the next steps? Any suggestion would be appreciated,
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