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Relative binding free energy between chemically distant compounds using a bidirectional non-equilibrium approach

<p>Data from &quot;Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach&quot;</p> <p>Submitted to J Chem Theory Comput, February &nbsp;2022.</p> <p>This archive contains the following directories:</p> <p><br> traj -&gt; This directory contains trajectory files for SAMPL9:</p> <p>&nbsp; &nbsp; &nbsp; &nbsp; g??_w.pdb.gz file contains ~ 160 snapshots from the 48 ns HREM sampling<br> &nbsp; &nbsp; &nbsp; &nbsp; of the target bound state of G1-G13 including water solvent.</p> <p>&nbsp; &nbsp; &nbsp; &nbsp; g??_1.pdb.gz file contains ~ 3500 snapshots (no solvent included) of the<br> &nbsp;&nbsp; &nbsp;target bound state of G1-G13</p> <p><br> work -&gt; This trajectory contains the work data (in kJ/mol) obtained in<br> &nbsp; &nbsp; &nbsp; &nbsp; the NE trajectories for SAMPL9:</p> <p>&nbsp;&nbsp; &nbsp;gxx-gyy_b_TIME.wrk is the work sample obtained for the xx-&gt;yy transmutation<br> &nbsp; &nbsp; &nbsp; &nbsp; in the bound state with a duration time of TIME.</p> <p>&nbsp;&nbsp; &nbsp;gxx-gyy_u_TIME.wrk is the work sample obtained for the xx-&gt;yy transmutation<br> &nbsp; &nbsp; &nbsp; &nbsp; in the unbound state with a duration time of TIME.</p> <p>pdb -&gt; This directory contains the pdb initial structures of the G1-G18 guests and the WP6 host</p> <p>ff -&gt; &nbsp;This directory contains the force field specification for SAMPL9:</p> <p>&nbsp;&nbsp; &nbsp;the PrimaDORAC generated (http://www1.chim.unifi.it/orac/primadorac/)<br> &nbsp; &nbsp; &nbsp; &nbsp; tpg and prm files for the guests and the host in orac format. &nbsp;(see<br> &nbsp; &nbsp; &nbsp; &nbsp; http://ftp.chim.unifi.it/orac/MAN/orac-manual.html)</p> <p>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> &nbsp; &nbsp; &nbsp; &nbsp;In order to compute an RBFE using the work data in the work dir, do the following:<br> &nbsp; &nbsp; &nbsp; &nbsp;1) cd into the bin directory<br> &nbsp; &nbsp; &nbsp; &nbsp;2) issue the command<br> &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;source source_this_file.bash<br> &nbsp;&nbsp; &nbsp; &nbsp;(N.B.: gfortran must be installed)<br> &nbsp; &nbsp; &nbsp; &nbsp;3) cd ../<br> &nbsp; &nbsp; &nbsp; &nbsp;4) from the main dir, issue the command:<br> &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;RBFE.bash -b 720 -u 360 B A<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; where &nbsp;B and A are the ghost and physical compound, respectively<br> &nbsp; &nbsp; &nbsp; &nbsp;Results for DG(A-&gt;B) are printed to the standard output</p> <p>&nbsp; &nbsp; &nbsp; &nbsp;Example: &nbsp; &nbsp; &nbsp;&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;RBFE.bash -b 720 -u 360 g01 g03 &gt; g03g01<br> &nbsp;&nbsp; &nbsp; &nbsp;In the g03g01 file, estimates and properties of the work data are<br> &nbsp;&nbsp; &nbsp; &nbsp;printed in the format<br> &nbsp;&nbsp; &nbsp; &quot;g05-&gt;g02 &nbsp; DG_bar= &nbsp; -5.13 &nbsp; 0.37 &nbsp;DG_ff_G= &nbsp; -4.2 &nbsp; 0.8 &nbsp;DG_ff_J= &nbsp; -3.0 &nbsp; 0.4 &nbsp;sig_AB_u= &nbsp;0.90 sig_AB_b= &nbsp;2.16 ADT_AB_u= &nbsp;0.26 ADT_AB_b= &nbsp;0.23 DG_rr_G= &nbsp;130.5 &nbsp;33.5 &nbsp;DG_rr_J= &nbsp; -7.2 &nbsp; 0.8 &nbsp;sig_BA_u= &nbsp;1.10 sig_BA_b= 13.61 ADT_BA_u= &nbsp;0.48 ADT_BA_b= &nbsp;3.40 &nbsp;DG_fr_G= &nbsp;-4.27 &nbsp;1.04 &nbsp;DG_fr_J= &nbsp;-3.23 &nbsp;0.58 bias_fr= &nbsp;0.2 &nbsp;DG_rf_G= 127.88 30.30 &nbsp;DG_rf_J= &nbsp;-7.16 &nbsp;0.66 bias_rf= &nbsp;0.0 DG_BAR= &nbsp;-5.26 0.0 tb= &nbsp;720 tu= &nbsp;360&quot;</p> <p>&nbsp;&nbsp; &nbsp; To compute all DDG estimates of Table 2 launch the script<br> &nbsp;&nbsp; &nbsp; &quot;do_all.bash&quot; from the main dir &nbsp;&nbsp;&nbsp; &nbsp; &nbsp;</p> <p>shift-pot -&gt; This directory contains two gnuplot scripts showing the evolution of the<br> &nbsp;&nbsp; &nbsp; &nbsp;Beutler LJ and elec soft-core potentials (soft.gplt) &nbsp;and of the shifted LJ and<br> &nbsp;&nbsp; &nbsp; &nbsp;elec soft-core potentials used in this work &nbsp;(shift.gplt)<br> &nbsp;</p>