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

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:

traj -> This directory contains trajectory files for SAMPL9:

        g??_w.pdb.gz file contains ~ 160 snapshots from the 48 ns HREM sampling
        of the target bound state of G1-G13 including water solvent.

        g??_1.pdb.gz file contains ~ 3500 snapshots (no solvent included) of the
    target bound state of G1-G13

work -> This trajectory contains the work data (in kJ/mol) obtained in
        the NE trajectories for SAMPL9:

    gxx-gyy_b_TIME.wrk is the work sample obtained for the xx->yy transmutation
        in the bound state with a duration time of TIME.

    gxx-gyy_u_TIME.wrk is the work sample obtained for the xx->yy transmutation
        in the unbound state with a duration time of TIME.

pdb -> This directory contains the pdb initial structures of the G1-G18 guests and the WP6 host

ff ->  This directory contains the force field specification for SAMPL9:

    the PrimaDORAC generated (http://www1.chim.unifi.it/orac/primadorac/)
        tpg and prm files for the guests and the host in orac format.  (see
        http://ftp.chim.unifi.it/orac/MAN/orac-manual.html)

bin -> This directory contains the script files to compute all bidirectional and unidirectional RBFE estimates as reported in Table 2 of the paper.
       In order to compute an RBFE using the work data in the work dir, do the following:
       1) cd into the bin directory
       2) issue the command
             source source_this_file.bash
       3) cd ../
       4) from the main dir, issue the command:
             RBFE.bash -b 720 -u 360 B A
          where  B and A are the ghost and physical compound, respectively
       Results for DG(A->B) are printed to the standard output

       Example:       
             RBFE.bash -b 720 -u 360 g01 g03 > g03g01
      In the g03g01 file, estimates and properties of the work data are
      printed in the format
     "g05->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
     "do_all.bash" from the main dir        

Nota bene: 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
instructions at http://www1.chim.unifi.it/orac/BUILDING.

shift-pot -> This directory contains two movies showing the evolution of the
      Beutler LJ and elec soft-core potentials (soft.mpg)  and of the shifted LJ and
      elec soft-core potentials used in this work  (shift.mpg)