Thermodynamic calculations-I

-


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 energies, standard deviations, and standard error of the mean for GB followed by PB. After each section, the ΔG of binding is given along with the error values. 
The final enthalpy for each GB and PB calculation are in section Differences (Complex - Receptor - Ligand). The first half of the file is GB calculations and the latter half is PB calculations. 



Comments

Post a Comment

Popular posts from this blog

Calculation of RMSD values between two ligand poses using web servers/tools

-
#Web servers for calculation of RMSD values between a ligand poses.  Please note: One pose should be a reference pose and another should be a query pose. PLDbench:  The RMSD value between two molecules can be calculated using PLDbench. There are four modules in this webserver. Single: This module's functionality is limited to calculating RMSD for the 57 complexes utilized in the benchmarking study. Users must submit the docked pose of a ligand that corresponds to one of the 57 PDB-IDs offered in the drop down option in this module. It accepts three file formats: '.pdb', '.mol2', and '.sdf'. Users can choose the type of RMSD they want to compute. Standard heavy-atom RMSD, Hungarian (symmetry-corrected) heavy-atom RMSD, and Minimum-distance heavy-atom RMSD can all be calculated using this module. As a result, the Hungarian (symmetry-corrected) heavy-atom RMSD value is returned by default.  Link for the server:https://webs.iiitd.edu.in/raghava/pldbench/single.p...
Read more

AMBER TUTORIAL-2: How to simulate a protein- ligand system: basic steps for md simulation in amber (AMBER 16)

-
BLOG #3  Hi Guys,           This is a new tutorial on how to simulate a protein-ligand system: basic steps using AMBER. Before we begin, I hope you have read our previous post on AMBER TUTORIAL-1, since I will only be providing additional information with the ligand here, rather than repeating the previous instructions. #To parameterize the ligand file, we start with Antechamber and then parmchck.  These are a series of tools for creating files for organic molecules and some protein metal centers, which can then be read into LEaP. Junmei Wang created the Antechamber suite, which is intended to be used in conjunction with the general AMBER force field (GAFF) (gaff.dat). This is the package's most crucial program. It can convert a variety of files and assign atomic charges and types to them as well. Sqm (or, alternatively, mopac or divcon), atomtype, am1bcc, bondtype, espgen, respgen, and prepgen are among the programs that antechamber runs in respo...
Read more

Python script to plot 3D FEL plots

-
Image
  # To plot FEL in 3D use this python script and run as python2.7 fel3d.py. Here the file uses gibbs.txt. therefore before running the script make sure u have the gibbs.txt in the same folder of this script or else provide the location of the script.  I have attached some images from my research article using the same script for 3D FEL plot These plots are published in  Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1 The 2D FEL scripts are also mentioned in the next blog:  Python script to plot 2D FEL Another point to consider is: when u r plotting FEL plots for multiple systems, make sure your color bar/gradient should be same in all the plots. So u can  change the values in vmax,  ax.set_zlim(0, 18),  ticks=range(0, 21, 2)) in the script below.  Like in my case the highest value was 18 in gibbs free energy (the z axis) in all the axis. therefore i mentioned 18 there...
Read more