I optimized the structure of protein through energy minimization in a spherical water box with 0.15 M NaCl to maintain the charge at neutral using the CHARMM 27 force field, Langevin force field and the conjugate gradient method using NAMD. The temperature, cutoff and time step were set at 310 K, 12.0 and 2.0 fs, respectively. After simulation, I got many files (such as .dcd, .BAK, .log, .vel, .coor, .xcs). Now, which file I should use as a protein input file in Autodock Vina for performing the molecular docking study on this optimized protein?
DCD files contain trajectory coordinates (snapshots) which you can convert into PDB files, which you can use as inputs for molecular docking. (Cluster the snapshots. Perform molecular docking on one representative of each cluster.)
NAMD dcd file contain coordinates. In you minimization I think you take last coordinates, Its good minimised. you upload charmm toplogy in VMD and then DCD file and save last coordinates.
.dcd file is coordinate trajectory output file. This file stores the trajectory of all atom position coordinates, .BAK is your dcd backup file, .vel file corresponds to velocities and .coor file is position coordinate file
For molecular docking, you need the coordinate file (.dcd or .coor). Just convert these files to pdb. For conversion you can use VMD.
.dcd file contains the coordinate trajectory. You can extract the pdb file using vmd or cpptraj program (AMBER package).
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