DL COMP BIOTECH

There are various tools for the identification of the pockets from the dynamic structures i.e, MD simulation traj 

The step-by-step tutorial for calculations are well elaborated in this link: http://ambermd.org/tutorials/advanced/tutorial3/ However, the purpose of this blog is to provide briefings on the main calculation steps. After MD trajectory: you need to source the amber.sh file before running any PBSA/GBSA calculations. source $AMBERHOME/amber.sh  for running the mm-gbsa/pbsa, run the following command: mpirun -np 6 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa16.in -o FINAL_RESULTS_MMPBSA16.dat -eo pbsa.csv -do decom.dat -deo decom.csv -sp comp_solv.prmtop -cp comp.prmtop -rp pro.prmtop -lp lig.prmtop -y md_100ns.nc here, both MM-GBSA and MM-PBSA calculations are performed. Their outputs are in the following files: FINAL_RESULTS_MMPBSA16.dat: contains the date/time, any warnings based on the values and files given, the mm-pbsa.in text, the files used by the script, the number of frames analyzed, and which PB solver (if any) was used. The rest of the statistics file includes all the average...

PCA analysis through CPPTRAJ module of AmberTools: > source $AMBERHOME/amber.sh > $AMBERHOME/bin/cpptraj > parm comp_solv.prmtop > trajin comp_150ns.nc > center > autoimage > rms first @CA mass > average crdset avg_set > createcrd traj_set > run > crdaction traj_set rms ref avg_set @CA > crdaction traj_set matrix covar :116-229@CA name pro_covar out covmat.dat #writes covariance matrix based on the selection of residues > runanalysis diagmatrix pro_covar out evecs.dat vecs 100 name myevecs nmwiz nmwizvecs 100 nmwizfile porcupine.nmd nmwizmask :116-229@CA #writes the information about 100 principal components (first 100 PCs) for that particular selection,  produces .nmd file that can be used to generate porcupine plots in normal mode wizard plugin of VMD. > runanalysis modes eigenval name myevecs out evalfrac.dat  gives output about the eigen values, fraction of contribution, cumulative contributions of  eigen vectors(or PCs) (in ...