DOI: 10.5281/zenodo.6127394
title: Relative binding free energy between chemically distant compounds using a bidirectional non-equilibrium approach

description: Data from "Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach" Submitted to J Chem Theory Comput, February 2022. This archive contains the following directories: <br> traj -&gt; This directory contains trajectory files for SAMPL9: g??_w.pdb.gz file contains ~ 160 snapshots from the 48 ns HREM sampling<br> of the target bound state of G1-G13 including water solvent. g??_1.pdb.gz file contains ~ 3500 snapshots (no solvent included) of the<br> target bound state of G1-G13 <br> work -&gt; This trajectory contains the work data (in kJ/mol) obtained in<br> the NE trajectories for SAMPL9: gxx-gyy_b_TIME.wrk is the work sample obtained for the xx-&gt;yy transmutation<br> in the bound state with a duration time of TIME. gxx-gyy_u_TIME.wrk is the work sample obtained for the xx-&gt;yy transmutation<br> in the unbound state with a duration time of TIME. pdb -&gt; This directory contains the pdb initial structures of the G1-G18 guests and the WP6 host ff -&gt; This directory contains the force field specification for SAMPL9: the PrimaDORAC generated (http://www1.chim.unifi.it/orac/primadorac/)<br> tpg and prm files for the guests and the host in orac format. (see<br> http://ftp.chim.unifi.it/orac/MAN/orac-manual.html) bin -&gt; This directory contains the script files to compute all bidirectional and unidirectional RBFE estimates as reported in Table 2 of the paper.<br> In order to compute an RBFE using the work data in the work dir, do the following:<br> 1) cd into the bin directory<br> 2) issue the command<br> source source_this_file.bash<br> 3) cd ../<br> 4) from the main dir, issue the command:<br> RBFE.bash -b 720 -u 360 B A<br> where B and A are the ghost and physical compound, respectively<br> Results for DG(A-&gt;B) are printed to the standard output Example: <br> RBFE.bash -b 720 -u 360 g01 g03 &gt; g03g01<br> In the g03g01 file, estimates and properties of the work data are<br> printed in the format<br> "g05-&gt;g02 DG_bar= -5.13 0.37 DG_ff_G= -4.2 0.8 DG_ff_J= -3.0 0.4 sig_AB_u= 0.90 sig_AB_b= 2.16 ADT_AB_u= 0.26 ADT_AB_b= 0.23 DG_rr_G= 130.5 33.5 DG_rr_J= -7.2 0.8 sig_BA_u= 1.10 sig_BA_b= 13.61 ADT_BA_u= 0.48 ADT_BA_b= 3.40 DG_fr_G= -4.27 1.04 DG_fr_J= -3.23 0.58 bias_fr= 0.2 DG_rf_G= 127.88 30.30 DG_rf_J= -7.16 0.66 bias_rf= 0.0 DG_BAR= -5.26 0.0 tb= 720 tu= 360" To compute all DDG estimates of Table 2 launch the script<br> "do_all.bash" from the main dir <strong><em>Nota bene</em>: </strong>DDG estimates do not include the FSC corrections. These are reported in Table 1 of Ref. https://arxiv.org/abs/2202.06720. To run the script RBFE.bash, the qq (Anderson Darling test) and bennett (BAR) programs are needed. They are available via orac. To install orac download the code from http://www1.chim.unifi.it/orac/ and follow the installation<br> instructions at http://www1.chim.unifi.it/orac/BUILDING. shift-pot -&gt; This directory contains two movies showing the evolution of the<br> Beutler LJ and elec soft-core potentials (soft.mpg) and of the shifted LJ and<br> elec soft-core potentials used in this work (shift.mpg)<br>