I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the same coordinate Put these two proteins in a box and run MD 100 nanoseconds, for validation this trick compare rmsd x-ray pose and Md pose. please help me ... -- Gromacs Users mailing list
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