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For virtual screening, what area of the receptor should be selected as the search box for the binding site, if the area around the bound ligand in the pdb is far away from the catalytic triad in...
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Are the terms "serotype" and "subtype" interchangeable?
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What is the difference between .rst, .rst7, .inpcrd, and .mdcrd coordinate files and between .prmtop and .parm7 topology files for Amber 14? Is there any advantage between using a certain file...
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I think that my complex has been moving out of the 12 A octahedron water box (TIP3PBOX) during the 35 ns simulation in Amber 14, since my RMSD from cpptraj isn't stable, and when I've tried to...
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For my 10 ns MD simulations for my protein-ligand complexes, I first created .prmtop topology and .inpcrd coordinate files in tleap with a 12 A water box (using the solvateoct command) and added...
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I created .prmtop topology and .inpcrd coordinate files in tleap, and then I ran minimization, heating, and equilibration steps, and then 10 ns of production with pmemd in AMBER 14 and created...
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