Using the official release v1.2.5 binary (vina_1.2.5_linux_x86_64) for --local_only or --score_only type of calculations, REMARK VINA RESULT is not written to PDBQT output. Instead, summary of energy is written in log (standard output).
It would be really helpful to also have REMARK VINA RESULT in the PDBQT outputs of these calculations so that Ringtail can process the outputs.
AutoDock Vina v1.2.5
#################################################################
# If you used AutoDock Vina in your work, please cite: #
# #
# J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli #
# AutoDock Vina 1.2.0: New Docking Methods, Expanded Force #
# Field, and Python Bindings, J. Chem. Inf. Model. (2021) #
# DOI 10.1021/acs.jcim.1c00203 #
# #
# O. Trott, A. J. Olson, #
# AutoDock Vina: improving the speed and accuracy of docking #
# with a new scoring function, efficient optimization and #
# multithreading, J. Comp. Chem. (2010) #
# DOI 10.1002/jcc.21334 #
# #
# Please see https://github.com/ccsb-scripps/AutoDock-Vina for #
# more information. #
#################################################################
Scoring function : vina
Rigid receptor: 1iep_receptor.pdbqt
Ligand: 1iep_ligand.pdbqt
Grid center: ligand center (autobox)
Grid size : ligand size + 4 A in each dimension (autobox)
Grid space : 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 1
Computing Vina grid ... done.
Performing local search ... done.
Estimated Free Energy of Binding : -13.259 (kcal/mol) [=(1)+(2)+(3)-(4)]
(1) Final Intermolecular Energy : -18.685 (kcal/mol)
Ligand - Receptor : -18.685 (kcal/mol)
Ligand - Flex side chains : 0.000 (kcal/mol)
(2) Final Total Internal Energy : -0.354 (kcal/mol)
Ligand : -0.354 (kcal/mol)
Flex - Receptor : 0.000 (kcal/mol)
Flex - Flex side chains : 0.000 (kcal/mol)
(3) Torsional Free Energy : 5.426 (kcal/mol)
(4) Unbound System's Energy : -0.354 (kcal/mol)
1iep_ligand_vinaloc_out.pdbqt
REMARK Flexibility Score: inf
REMARK Active torsions [ 7 ] -> [ 7 ]
ROOT
ATOM 1 C1 LIG L 1 15.851 54.716 12.336 1.00 0.00 0.038 A
ATOM 2 C2 LIG L 1 16.971 54.606 11.392 1.00 0.00 -0.029 A
ATOM 3 C3 LIG L 1 17.944 53.575 11.612 1.00 0.00 0.007 A
ATOM 4 C4 LIG L 1 17.819 52.672 12.730 1.00 0.00 0.024 A
ATOM 5 C5 LIG L 1 16.731 52.774 13.646 1.00 0.00 0.035 A
ATOM 6 C6 LIG L 1 15.743 53.819 13.429 1.00 0.00 0.047 A
ATOM 7 C7 LIG L 1 17.151 55.541 10.174 1.00 0.00 0.045 C
ENDROOT
BRANCH 1 8
ATOM 8 N1 LIG L 1 14.874 55.701 12.175 1.00 0.00 -0.283 N
ATOM 9 H1 LIG L 1 13.995 55.459 11.803 1.00 0.00 0.155 HD
BRANCH 8 10
ATOM 10 C8 LIG L 1 15.127 57.016 12.535 1.00 0.00 0.220 A
ATOM 11 C9 LIG L 1 14.302 59.243 12.716 1.00 0.00 0.077 A
ATOM 12 C10 LIG L 1 15.565 59.695 13.224 1.00 0.00 0.048 A
ATOM 13 N2 LIG L 1 14.132 57.915 12.392 1.00 0.00 -0.214 NA
ATOM 14 C11 LIG L 1 16.590 58.733 13.365 1.00 0.00 0.116 A
ATOM 15 N3 LIG L 1 16.358 57.419 13.021 1.00 0.00 -0.223 NA
BRANCH 11 16
ATOM 16 C12 LIG L 1 13.123 60.141 12.507 1.00 0.00 0.019 A
ATOM 17 C13 LIG L 1 11.915 62.341 12.760 1.00 0.00 0.020 A
ATOM 18 C14 LIG L 1 13.078 61.516 12.989 1.00 0.00 0.013 A
ATOM 19 C15 LIG L 1 10.802 61.769 12.047 1.00 0.00 0.111 A
ATOM 20 N4 LIG L 1 10.857 60.445 11.586 1.00 0.00 -0.263 NA
ATOM 21 C16 LIG L 1 11.964 59.628 11.790 1.00 0.00 0.120 A
ENDBRANCH 11 16
ENDBRANCH 8 10
ENDBRANCH 1 8
BRANCH 5 22
ATOM 22 N5 LIG L 1 16.669 51.830 14.734 1.00 0.00 -0.281 N
ATOM 23 C17 LIG L 1 15.711 51.740 15.730 1.00 0.00 0.248 C
ATOM 24 H2 LIG L 1 17.397 51.168 14.773 1.00 0.00 0.155 HD
ATOM 25 O1 LIG L 1 14.872 52.598 15.961 1.00 0.00 -0.270 OA
BRANCH 23 26
ATOM 26 C18 LIG L 1 15.691 50.529 16.606 1.00 0.00 0.037 A
ATOM 27 C19 LIG L 1 14.531 50.216 17.444 1.00 0.00 0.013 A
ATOM 28 C20 LIG L 1 16.849 49.661 16.628 1.00 0.00 0.013 A
ATOM 29 C21 LIG L 1 14.544 49.051 18.292 1.00 0.00 0.002 A
ATOM 30 C22 LIG L 1 16.859 48.519 17.460 1.00 0.00 0.002 A
ATOM 31 C23 LIG L 1 15.723 48.188 18.305 1.00 0.00 -0.064 A
BRANCH 31 32
ATOM 32 C24 LIG L 1 15.833 46.936 19.195 1.00 0.00 -0.043 C
BRANCH 32 33
ATOM 33 N6 LIG L 1 17.084 46.774 19.996 1.00 0.00 0.380 N
ATOM 34 C25 LIG L 1 17.279 47.953 20.918 1.00 0.00 -0.097 C
ATOM 35 C26 LIG L 1 17.086 45.471 20.800 1.00 0.00 -0.097 C
ATOM 36 H3 LIG L 1 17.860 46.732 19.335 1.00 0.00 -0.082 HD
ATOM 37 C27 LIG L 1 18.587 47.813 21.746 1.00 0.00 -0.098 C
ATOM 38 C28 LIG L 1 18.411 45.307 21.614 1.00 0.00 -0.098 C
ATOM 39 N7 LIG L 1 18.591 46.513 22.537 1.00 0.00 0.375 N
ATOM 40 C29 LIG L 1 19.806 46.334 23.346 1.00 0.00 -0.096 C
ATOM 41 H4 LIG L 1 17.801 46.576 23.179 1.00 0.00 -0.082 HD
ENDBRANCH 32 33
ENDBRANCH 31 32
ENDBRANCH 23 26
ENDBRANCH 5 22
TORSDOF 7
Using the official release v1.2.5 binary (vina_1.2.5_linux_x86_64) for
--local_onlyor--score_onlytype of calculations,REMARK VINA RESULTis not written to PDBQT output. Instead, summary of energy is written in log (standard output).It would be really helpful to also have
REMARK VINA RESULTin the PDBQT outputs of these calculations so that Ringtail can process the outputs.Example inputs: 1iep_ligand.pdbqt 1iep_receptor.pdbqt
Commands:
Outputs: loc_out.log
1iep_ligand_vinaloc_out.pdbqt