Computational Drug Discovery and Design
time the minimization includes solute under weak restraints (force constant equal to 10 kcal/mol/A ̊^2 ): Initial energy minimiz ...
integration step of 2 fs. It is during this simulation that the system starts shrinking if the initial density was not optimal: ...
huge output trajectory files. It is for this reason that we use the NetCDF format, which roughly halves the original volume of t ...
MDlast=$Njobs MDcurr=$MDfirst MDinp=0 while [ $MDcurr -le $MDlast ] do echo -n "Job $MDcurr started on " date let "MDinp = ${MDc ...
systems require long computation times, often weeks to months long. If a power failure occurs, the MD run is termi- nated premat ...
To obtain the same result with the newer command cpptraj (Amber 14) add the keyword multi at the end of the last line. The examp ...
if( $numfil != 0)then foreach fnam (${DIR}/.pdb.?) set fr=$fnam:r set fnum=$fnam:e mv $fnam $fr.0000$fnum echo $fnam $fr.0000$fn ...
getline;centind=index($0,"#Centroid"); } numcent=0; print $2,$1,NR-b0; c=$2; getline; endrec = index("End",$0); while( endrec != ...
3.5 Virtual Screening of Ligands and Multiple Receptor Structures In this chapter, we will deal with two possible virtual screen ...
The “cleaned” chemical library is then submitted to rigid- receptor docking on a set of receptor’s representative structures (e ...
(http://openmp.org) and it works on shared memory architec- tures. In order to use it with chemical libraries containing large n ...
vina --config vina.conf --cpu 1 --ligand \$LIGAND \ --out ${outdir}/\${lnam}_out.pdbqt \ --log ${outdir}/\${lnam}_log.dat END # ...
echo $nrj $fnam>>x_tmp; i=‘expr $i + 1‘; done sort -n –k1 x_tmp>sorted_NRG rm x_tmp The output file sorted_NRG contains ...
In the next step, use tleap to create topology and coordinate files for the ligand. The following script shows an example of tle ...
Launch MD simulation following the recipes in Subheadings 3.2and 3.3. The procedures for the complex are identical as for the r ...
containing RMSF of atomic fluctuations. Finally, there remains the question of intermolecular contacts. These can be obtained fr ...
# Terminal residues have different atom names donor mask @OXT acceptor mask :1@N :1@H1 acceptor mask :1@N :1@H2 acceptor mask :1 ...
the protein and of the ligand. In practice, this information is extracted from the MD trajectory of the solvated protein–ligand ...
then LIGFILE="lig.prmtop" fi echo -n "Trajectory file (name with ext.): " read MDCRD if [ -z "$MDCRD" ] then echo "*** Error: Tr ...
/ &gb # for igb=5, use "set default PBradii mbondi2" # in scripts producing prmtop files # for igb=7, use "set default PBrad ...
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