Mon Oct 10 14:02:16 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 Mon Oct 10 2011 at 14:02:17 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: HIZ 64 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 786 has a net charge of 1.4000 !!! WARNING: ZN7 787 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6165997 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): -10.61700 38.72700 ymin,ymax (A): -21.87700 25.22500 zmin,zma (A): -12.53000 45.20600 x,y,z range (A): 49.34400 47.10200 57.73600 scale (grids/A): 0.6165997 object centre (A): 14.05500 1.674001 16.33800 number of atom coordinates read : 2577 total number of charged atoms : 2455 net assigned charge : 5.100009 assigned positive charge : 394.0040 centred at (gu) : 88.52657 89.03452 89.59735 assigned negative charge : -388.9046 centred at (gu) : 88.40987 89.07571 89.49714 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6364 nv = 96 ne = 84 npr = 53703 no. pairs analyzed = 53703 no. exposed pairs = 3035 no. arc points = 21903 no. surface atoms = 1015 nbur = 1562 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3511 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3300000 number of dielectric boundary points 3140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7997 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5165205E-09 8.9353289E-09 midg,1,midg; midg,igrid,midg 7.7592777E-09 1.1004498E-09 1,midg,midg; igrid,midg,midg -4.7012683E-09 7.7656326E-09 gauss-seidel spectral radius is 0.9863747 estimated iterations to convergence 70 setup time was (sec) 0.5600000 now iterating at: 14:02:17 rms-change max change #iterations 0.1225804 19.73570 at 10iterations 1.1151129E-02 1.989964 at 20iterations 1.0020988E-03 0.1699219 at 30iterations 9.3326176E-05 1.5688896E-02 at 40iterations 8.4512112E-06 1.3275146E-03 at 50iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 8.4512112E-06 1.3275146E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 14:02:21 3.281u 0.172s 0:04.53 76.1% 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 Mon Oct 10 2011 at 14:02:21 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: HIZ 64 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 786 has a net charge of 1.4000 !!! WARNING: ZN7 787 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.849799 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): -10.61700 38.72700 ymin,ymax (A): -21.87700 25.22500 zmin,zma (A): -12.53000 45.20600 x,y,z range (A): 49.34400 47.10200 57.73600 scale (grids/A): 1.849799 object centre (A): 14.05500 1.674001 16.33800 number of atom coordinates read : 2577 total number of charged atoms : 2455 net assigned charge : 5.100009 assigned positive charge : 394.0040 centred at (gu) : 85.57906 87.10304 88.79157 assigned negative charge : -388.9046 centred at (gu) : 85.22923 87.22672 88.49122 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21903 grid for indexing accessible points = 1.400000 m= 23797 mr = 48158 m= 3387 mr = 17561 m= 147 mr = 2000 m= 0 mr = 32 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 4120 time to turn everything in is 0.5500000 number of dielectric boundary points 28939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19247 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) : 0.6165997 object centre at (A) : 14.05500 1.674001 16.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5073781E-02 2.2789119E-02 midg,1,midg; midg,igrid,midg 1.2618109E-02 4.1342271E-03 1,midg,midg; igrid,midg,midg -1.1063498E-03 3.6712293E-02 gauss-seidel spectral radius is 0.9985493 estimated iterations to convergence 208 setup time was (sec) 0.8200000 now iterating at: 14:02:23 rms-change max change #iterations 4.005570 172.1308 at 10iterations 1.832174 59.81246 at 20iterations 0.8332756 29.55422 at 30iterations 0.3838052 12.29491 at 40iterations 0.1747495 5.344173 at 50iterations 8.0274865E-02 2.642740 at 60iterations 3.6792822E-02 1.259438 at 70iterations 1.6755577E-02 0.5877843 at 80iterations 7.6997387E-03 0.2680588 at 90iterations 3.5122375E-03 0.1212902 at 100iterations 1.6081840E-03 5.3130150E-02 at 110iterations 7.3553692E-04 2.3689270E-02 at 120iterations finished qdiffx linear iterations at : 14:02:29 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 7.3553692E-04 2.3689270E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 14:02:30 7.299u 0.202s 0:08.56 87.5% 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 Mon Oct 10 2011 at 14:02:30 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: HIZ 64 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 786 has a net charge of 1.4000 !!! WARNING: ZN7 787 has a net charge of 1.4000 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: 2.774699 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): -10.61700 38.72700 ymin,ymax (A): -21.87700 25.22500 zmin,zma (A): -12.53000 45.20600 x,y,z range (A): 49.34400 47.10200 57.73600 scale (grids/A): 2.774699 object centre (A): 14.05500 1.674001 16.33800 number of atom coordinates read : 2577 total number of charged atoms : 2455 net assigned charge : 5.100009 assigned positive charge : 394.0040 centred at (gu) : 83.36845 85.65456 88.18717 assigned negative charge : -388.9046 centred at (gu) : 82.84368 85.84004 87.73675 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 160562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21903 grid for indexing accessible points = 1.400000 m= 79012 mr = 116745 m= 26669 mr = 64698 m= 5942 mr = 21315 m= 677 mr = 4354 m= 22 mr = 369 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 14522 time to turn everything in is 1.180000 number of dielectric boundary points 65397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 19634 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) : 1.849799 object centre at (A) : 14.05500 1.674001 16.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0201508E-02 0.2926636 midg,1,midg; midg,igrid,midg 0.1548756 5.3522468E-02 1,midg,midg; igrid,midg,midg -3.7070505E-02 0.4687915 gauss-seidel spectral radius is 0.9992293 estimated iterations to convergence 284 setup time was (sec) 1.450000 now iterating at: 14:02:32 rms-change max change #iterations 9.415190 330.0462 at 10iterations 5.404245 150.5833 at 20iterations 3.078551 72.85071 at 30iterations 1.753311 36.33670 at 40iterations 0.9973617 20.30048 at 50iterations 0.5658175 10.86446 at 60iterations 0.3219457 6.203437 at 70iterations 0.1826536 3.433655 at 80iterations 0.1037788 1.985931 at 90iterations 5.9000764E-02 1.157688 at 100iterations 3.3361875E-02 0.6037083 at 110iterations 1.8945407E-02 0.3549876 at 120iterations 1.0743142E-02 0.2062187 at 130iterations 6.0942518E-03 0.1154690 at 140iterations 3.4562498E-03 6.0836792E-02 at 150iterations 1.9596908E-03 3.6124229E-02 at 160iterations 1.1124961E-03 2.1155357E-02 at 170iterations 6.3188246E-04 1.1709213E-02 at 180iterations finished qdiffx linear iterations at : 14:02:42 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 6.3188246E-04 1.1709213E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 14:02:43 11.351u 0.185s 0:12.01 96.0% 0+0k 0+0io 0pf+0w