ADL: (no subject)

malihe ebrahimi maliheheb at yahoo.com
Sun Oct 23 05:02:58 PDT 2011





________________________________

Hi 
I have one question from out-put of autodock,please answer and help  me:
In output of autodock ,we found 'q' in bottom of rank = 1 what is it? our molecule has zero charge but after docking has charge ( not zreo)
example:
 USER Cluster Rank = 1
USER Number of conformations in this cluster = 1
USERUSER RMSD from reference structure = 12.901 A
USERUSER Estimated Free Energy of Binding = -8.03 kcal/mol [=(1)+(2)+(3)-(4)]USER Estimated Inhibition Constant, Ki = 1.31 uM (micromolar) [Temperature = 298.15 K]USERUSER (1) Final Intermolecular Energy = -9.52 kcal/mol
USER vdW + Hbond + desolv Energy = -9.47 kcal/mol
USER Electrostatic Energy = -0.05 kcal/mol
USER (2) Final Total Internal Energy = -0.52 kcal/mol
USER (3) Torsional Free Energy = +1.49 kcal/mol
USER (4) Unbound System's Energy [=(2)] = -0.52 kcal/mol
USERUSERUSERUSER DPF = 14n.dpf
USER NEWDPF move
USER NEWDPF about14n.pdbqt-1.022200 -1.355600 -0.848800USER NEWDPF tran05.295206 8.420807 7.471953USER NEWDPF axisangle0-0.811959 0.334578 -0.478310 158.988571USER NEWDPF quaternion0-0.798348 0.328969 -0.470291 0.182334USER NEWDPF dihe0159.40 -108.11 117.81 117.85 -3.90 USERATOM 1 N MOL A 0 7.888 12.319 3.340 -0.51 +0.04 -0.221 12.901
ATOM 2 C MOL A 0 8.295 13.017 4.423 -0.44 -0.00 +0.258 12.901
ATOM 3 C MOL A 0 7.160 11.339 3.915 -0.39 -0.02 +0.151 12.901
ATOM 4 N MOL A 0 7.877 12.544 5.611 -0.32 -0.05-0.160 12.901
ATOM 5 N MOL A 0 7.153 11.468 5.246 -0.29 -0.04 -0.225 12.901
ATOM 6 C MOL A 0 6.520 10.331 3.318 -0.09 -0.01+0.053 12.901
ATOM 7 C MOL A 0 5.856 9.454 4.089 -0.39 -0.00 +0.017 12.901
ATOM 8 C MOL A 0 5.790 9.555 5.434 -0.33 -0.00-0.004 12.901
ATOM 9 C MOL A 0 6.484 10.570 5.988 -0.26 +0.04 +0.133 12.901
ATOM 10 C MOL A 0 5.120 8.675 6.214 -0.28 +0.00+0.026 12.901
ATOM 11 C MOL A 0 5.516 8.422 7.482 -0.23 +0.01 +0.136 12.901
ATOM 12 N MOL A 0 4.732 7.458 7.986 -0.18 +0.02 -0.217 12.901
ATOM 13 N MOL A 0 3.810 7.127 7.057 -0.18 +0.01 -0.163 12.901
ATOM 14 C MOL A 0 4.043 7.884 5.960 -0.22 -0.00 +0.118 12.901
ATOM 15 C MOL A 0 3.147 7.817 4.956 -0.25 -0.00+0.088 12.901
ATOM 16 C MOL A 0 2.161 6.896 4.938 -0.25 -0.00+0.034 12.901
ATOM 17 N MOL A 0 3.151 8.702 4.052 -0.19 +0.01 -0.252 12.901
ATOM 18 C MOL A 0 1.239 6.907 3.962 -0.36 -0.00 +0.004 12.901
ATOM 19 C MOL A 0 1.317 7.857 3.020 -0.40 -0.00+0.027 12.901
ATOM 20 C MOL A 0 2.312 8.753 3.109 -0.40 -0.00 +0.031 12.901
ATOM 21 C MOL A 0 2.493 9.874 2.121 -0.39 -0.00 +0.070 12.901
ATOM 22 C MOL A 0 4.841 6.979 9.238 -0.36 -0.04 +0.199 12.901
ATOM 23 S MOL A 0 6.311 6.295 9.730 -0.53 +0.01-0.039 12.901
ATOM 24 N MOL A 0 3.718 6.755 9.942 -0.11 +0.12 -0.332 12.901
ATOM 25 H MOL A 0 3.917 6.367 10.863 -0.29 -0.10 +0.168 12.901
ATOM 26 C MOL A 0 2.678 7.610 9.927 -0.22 -0.01 +0.034 12.901
ATOM 27 C MOL A 0 1.493 7.176 9.472 -0.20 -0.00 +0.032 12.901
ATOM 28 C MOL A 0 0.443 8.010 9.442 -0.16 -0.00 +0.039 12.901
ATOM 29 C MOL A 0 0.527 9.291 9.844 -0.25 -0.00 +0.068 12.901
ATOM 30 C MOL A 0 1.735 9.710 10.274 -0.24 +0.00+0.039 12.901
ATOM 31 C MOL A 0 2.798 8.891 10.312 -0.22 -0.00 +0.032 12.901
ATOM 32 O MOL A 0 -0.603 10.062 9.775 -0.26 +0.03 -0.356 12.901
ATOM 33 C MOL A 0 -1.660 9.667 8.936 -0.26 -0.02 +0.210 12.901
TER
ENDMDLUSER                            x         y        z        vdW  Elec    q         RMS


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