Dear Gromacs users!
I want to simulate membrane receptor in the Gromos 56 force field in the vacuu and I have some methodological questions. 1- I need to edit topology of my structure by adding one DOUBLE covalent bond between desires atoms ( they have been already placed in the desired adjacent positions by pymol). I add string in topology.top [bonds] 2809 2810 2 gb_5 Does it enough? What addition modification of the topology file requires for the addition covalent bond? Where I could found names of all bonds parametrs such as gb_5 ? I've found that number for the C=O pair so as I understood this must correspond to double planar bond. 2- I've received message that my system consist of 2 negative charges. For water-souluble proteins I just place 2 counter ions in the SOLVENT to neitralize this charge. What I should do for the vacuu simulation ? Thanks! James
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