Tue Oct 11 06:08:04 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:08:04 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7492529 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 1.829000 40.92600 ymin,ymax (A): -26.27700 17.66200 zmin,zma (A): 38.09500 85.60900 x,y,z range (A): 39.09700 43.93900 47.51400 scale (grids/A): 0.7492529 object centre (A): 21.37750 -4.307500 61.85200 number of atom coordinates read : 2016 total number of charged atoms : 1878 net assigned charge : 5.837007 assigned positive charge : 304.9302 centred at (gu) : 88.29890 90.08591 91.17190 assigned negative charge : -299.0932 centred at (gu) : 88.24797 90.28764 91.22192 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7744 nv = 96 ne = 84 npr = 41103 no. pairs analyzed = 41103 no. exposed pairs = 2432 no. arc points = 16586 no. surface atoms = 833 nbur = 1183 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 583 mr = 4516 m= 6 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1490 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8162 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4892053E-07 8.5476053E-08 midg,1,midg; midg,igrid,midg 3.4713500E-07 -1.0879781E-07 1,midg,midg; igrid,midg,midg 9.2128822E-08 1.3623043E-07 gauss-seidel spectral radius is 0.9906984 estimated iterations to convergence 84 setup time was (sec) 0.5200000 now iterating at: 06:08:05 rms-change max change #iterations 0.2472307 33.19621 at 10iterations 3.5020355E-02 4.513172 at 20iterations 4.9141590E-03 0.7846260 at 30iterations 7.5152004E-04 9.5199585E-02 at 40iterations 1.4804598E-04 1.6296387E-02 at 50iterations finished qdiffx linear iterations at : 06:08:08 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.4804598E-04 1.6296387E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:08:08 3.366u 0.180s 0:04.01 88.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:08:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.247759 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 1.829000 40.92600 ymin,ymax (A): -26.27700 17.66200 zmin,zma (A): 38.09500 85.60900 x,y,z range (A): 39.09700 43.93900 47.51400 scale (grids/A): 2.247759 object centre (A): 21.37750 -4.307500 61.85200 number of atom coordinates read : 2016 total number of charged atoms : 1878 net assigned charge : 5.837007 assigned positive charge : 304.9302 centred at (gu) : 84.89674 90.25811 93.51589 assigned negative charge : -299.0932 centred at (gu) : 84.74391 90.86291 93.66578 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16586 grid for indexing accessible points = 1.400000 m= 34472 mr = 58053 m= 7390 mr = 26599 m= 859 mr = 5172 m= 30 mr = 501 m= 0 mr = 3 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 33639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14961 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7492529 object centre at (A) : 21.37750 -4.307500 61.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7688741E-02 1.6089331E-02 midg,1,midg; midg,igrid,midg 8.1538633E-02 1.1708927E-03 1,midg,midg; igrid,midg,midg 3.5705741E-02 1.6928086E-02 gauss-seidel spectral radius is 0.9989307 estimated iterations to convergence 242 setup time was (sec) 0.9300000 now iterating at: 06:08:10 rms-change max change #iterations 5.006574 180.0217 at 10iterations 2.560709 82.50815 at 20iterations 1.315548 38.49432 at 30iterations 0.6765157 21.43733 at 40iterations 0.3463258 11.13659 at 50iterations 0.1778885 4.909912 at 60iterations 9.1089979E-02 2.549112 at 70iterations 4.6671525E-02 1.233721 at 80iterations 2.3949711E-02 0.7245350 at 90iterations 1.2362633E-02 0.3726954 at 100iterations 6.3942219E-03 0.1824799 at 110iterations 3.3169740E-03 9.0423584E-02 at 120iterations finished qdiffx linear iterations at : 06:08:17 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 3.3169740E-03 9.0423584E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 06:08:17 8.176u 0.240s 0:08.92 94.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:08:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.371638 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 1.829000 40.92600 ymin,ymax (A): -26.27700 17.66200 zmin,zma (A): 38.09500 85.60900 x,y,z range (A): 39.09700 43.93900 47.51400 scale (grids/A): 3.371638 object centre (A): 21.37750 -4.307500 61.85200 number of atom coordinates read : 2016 total number of charged atoms : 1878 net assigned charge : 5.837007 assigned positive charge : 304.9302 centred at (gu) : 82.34525 90.38719 95.27392 assigned negative charge : -299.0932 centred at (gu) : 82.11599 91.29440 95.49869 start vw surface at 0.1500000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 187061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16586 grid for indexing accessible points = 1.400000 m= 104834 mr = 139292 m= 45800 mr = 88238 m= 14398 mr = 38345 m= 3303 mr = 11410 m= 533 mr = 2517 m= 36 mr = 383 m= 0 mr = 13 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 75767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 15024 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.247759 object centre at (A) : 21.37750 -4.307500 61.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3244837 9.1038868E-02 midg,1,midg; midg,igrid,midg 0.5835760 -5.2572261E-03 1,midg,midg; igrid,midg,midg 0.3939175 0.1230557 gauss-seidel spectral radius is 0.9993214 estimated iterations to convergence 303 setup time was (sec) 2.430000 now iterating at: 06:08:20 rms-change max change #iterations 10.86782 345.7107 at 10iterations 6.492975 178.4735 at 20iterations 3.865142 80.01732 at 30iterations 2.300685 44.94031 at 40iterations 1.365866 21.71564 at 50iterations 0.8083938 15.05016 at 60iterations 0.4783871 7.947070 at 70iterations 0.2834017 4.832016 at 80iterations 0.1677386 2.934654 at 90iterations 9.9277616E-02 1.585321 at 100iterations 5.8693808E-02 0.9448242 at 110iterations 3.4854919E-02 0.5787354 at 120iterations 2.0792292E-02 0.3474007 at 130iterations 1.2506231E-02 0.2175303 at 140iterations 7.6672169E-03 0.1212730 at 150iterations 4.8481533E-03 9.1049194E-02 at 160iterations 3.1854785E-03 5.8761597E-02 at 170iterations 2.2064217E-03 4.1580200E-02 at 180iterations finished qdiffx linear iterations at : 06:08:31 total time elapsed so far: 13.74000 # loops : 180 mean,max change (kT/e) : 2.2064217E-03 4.1580200E-02 energy calculations done at 13.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 06:08:33 13.953u 0.227s 0:15.29 92.6% 0+0k 0+0io 0pf+0w