source leaprc.constph source leaprc.conste # Load parameters for ions loadAmberParams frcmod.ionsjc_tip3p # Load PDB mp8 = loadpdb NAcMP8.constphe.pdb # Connecting HEH to the protein bond mp8.14.CB2 mp8.2.CA bond mp8.14.CB1 mp8.9.CA bond mp8.14.CBC1 mp8.8.CA bond mp8.14.CBB2 mp8.5.CA # Connecting HEH to the PRNs bond mp8.14.C3D mp8.16.CA bond mp8.14.C2A mp8.15.CA # Solvate solvateOct mp8 TIP3PBOX 10.0 # Add ions addIonsRand mp8 Na+ 2 # Save topology and coordinate files saveamberparm mp8 mp8_es.prmtop mp8_es.rst7 # Quit quit