Update README.md

input_files/BRD4/README.md

@@ -6,7 +6,7 @@ This set of files comprises PDB, sd, and mol2 files for all the benchmark ligand
 
 ## Methods
 
-The structures for all ligands except Compound 8a (a non-binder) were obtained directly from their co-crystal structures with BRD4(1), which are identified in Table 7. The structure of Compound 8a was downloaded from the PubChem database with CID 2295889. All ligands have zero charge, and the hydrogens were added using openbabel [1]. The partial charges for the ligand atoms were assigned using antechamber [2] with the AM1-BCC charge model [3], generating a mol2 file, which was then converted to the pdb and sd formats using openbabel. The partial charges for the apo BRD4 (in the 4lyi.mol2 file), were assigned according to the AMBERff14SB protein force-field [4]. The starting configurations for all the solvated complexes, except BRD4(1) bound to Compound 8a, were obtained directly from their respective co-crystal structures. In the case of Compound 8a, the latter was docked into the apo BRD4(1) using AutoDock Vina [5], generating a similar binding mode as Compound 4. All ions/molecules besides the protein and ligand were removed before solvation. The parameters for the protein were obtained from the AMBERff14SB protein force-field, and the partial charges for the ligands as described above. The bonded and Lennard-Jones parameters for the ligands were obtained from the Amber General Force Field (GAFF) [6], also using antechamber. Each solvated complex has 11000 TIP3P water molecules with 32 Na+ and 35 Cl- ions (0.15 M NaCl), with TIP3P-specific ion parameters from Joung and Cheatham [7].
+The structures for all ligands except Compound 8a (a non-binder) were obtained directly from their co-crystal structures with BRD4(1), which are identified in Table 7. The initial structure of Compound 8a was downloaded from the PubChem database with CID 2295889. All ligands have zero charge, and the hydrogens were added using openbabel [1]. The partial charges for the ligand atoms were assigned using antechamber [2] with the AM1-BCC charge model [3], generating a mol2 file, which was then converted to the pdb and sd formats using openbabel. The partial charges for the apo BRD4 (in the 4lyi.mol2 file), were assigned according to the AMBERff14SB protein force-field [4]. The starting configurations for all the solvated complexes, except BRD4(1) bound to Compound 8a, were obtained directly from their respective co-crystal structures. In the case of Compound 8a, the latter was docked into the apo BRD4(1) using AutoDock Vina [5], generating a similar binding mode as Compound 4. All ions/molecules besides the protein and ligand were removed before solvation. The parameters for the protein were obtained from the AMBERff14SB protein force-field, and the partial charges for the ligands as described above. The bonded and Lennard-Jones parameters for the ligands were obtained from the Amber General Force Field (GAFF) [6], also using antechamber. Each solvated complex has 11000 TIP3P water molecules with 32 Na+ and 35 Cl- ions (0.15 M NaCl), with TIP3P-specific ion parameters from Joung and Cheatham [7].
 
 ## References