Dear all,
I have some question about the setbox, ChBox and box dimension and angle.
I’m running TI simulations. First the protein-single ligand complex is solvated using solvateoct, which creates a truncated octahedron box. Then classical MD is performed on this protein-single ligand system. Then a pdb is generated from the equilibrated rst file, and another ligand was added to the pdb (protein-dual ligand pdb). Now if I want to use the protein-dual ligand pdb to generate topology, that still remains the truncated octahedron box, is the following procedure correct?
1) load the protein-dual ligand pdb to tleap, and use "setbox a centers” to generate topologies: A.prmtop, A.inpcrd; the box angle would be 90 degrees.
2) use ChBox to change the box angel of A.inpcrd to 109.471219 degrees, and still remain the same box dimension; generates A_modified.inpcrd.
3) Should I also change the box angle in the A.prmtop file?
Or another way of doing it is in the beginning just solvate the protein-single ligand complex with solvatebox, which creates a cubic box. And later on just do step 1) above to generate the dual ligand topology. Correct? But this may slow down the calculation a bit since there’re more waters.
Thanks!
Best,
Lin
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Received on Thu Mar 07 2019 - 10:00:03 PST
