Mon Oct 10 17:10:25 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 17:10:25 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIZ 66 has a net charge of 0.2000 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIY 94 has a net charge of 0.2000 !!! WARNING: HIZ 116 has a net charge of 0.2000 !!! WARNING: HIZ 120 has a net charge of 0.2000 !!! WARNING: HIZ 126 has a net charge of 0.2000 !!! WARNING: HIZ 541 has a net charge of 0.2000 !!! WARNING: HIY 569 has a net charge of 0.2000 !!! WARNING: ZN6 632 has a net charge of 1.4000 !!! WARNING: ZN6 633 has a net charge of 1.4000 !!! WARNING: ZN6 639 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6611693 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): -7.815000 33.18000 ymin,ymax (A): 35.16100 88.96500 zmin,zma (A): 17.17000 71.01400 x,y,z range (A): 40.99500 53.80400 53.84400 scale (grids/A): 0.6611693 object centre (A): 12.68250 62.06300 44.09200 number of atom coordinates read : 2089 total number of charged atoms : 1960 net assigned charge : -1.699992 assigned positive charge : 305.4449 centred at (gu) : 89.29758 90.67355 89.01579 assigned negative charge : -307.1449 centred at (gu) : 89.29261 90.77192 88.76890 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 43135 no. pairs analyzed = 43135 no. exposed pairs = 2827 no. arc points = 20953 no. surface atoms = 938 nbur = 1151 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 349 mr = 3095 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.4000000 number of dielectric boundary points 3451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1897 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4999976E-08 2.8323074E-08 midg,1,midg; midg,igrid,midg 1.0245005E-08 -2.2839155E-08 1,midg,midg; igrid,midg,midg -5.3256173E-09 -2.6390172E-09 gauss-seidel spectral radius is 0.9881070 estimated iterations to convergence 75 setup time was (sec) 0.7000000 now iterating at: 17:10:26 rms-change max change #iterations 0.1590188 25.90191 at 10iterations 1.6668295E-02 2.367929 at 20iterations 1.7891155E-03 0.2569942 at 30iterations 1.9456126E-04 3.4507751E-02 at 40iterations 2.1553411E-05 3.1762123E-03 at 50iterations finished qdiffx linear iterations at : 17:10:30 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 2.1553411E-05 3.1762123E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 17:10:30 4.558u 0.395s 0:05.25 94.0% 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 17:10:30 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIZ 66 has a net charge of 0.2000 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIY 94 has a net charge of 0.2000 !!! WARNING: HIZ 116 has a net charge of 0.2000 !!! WARNING: HIZ 120 has a net charge of 0.2000 !!! WARNING: HIZ 126 has a net charge of 0.2000 !!! WARNING: HIZ 541 has a net charge of 0.2000 !!! WARNING: HIY 569 has a net charge of 0.2000 !!! WARNING: ZN6 632 has a net charge of 1.4000 !!! WARNING: ZN6 633 has a net charge of 1.4000 !!! WARNING: ZN6 639 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.983508 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): -7.815000 33.18000 ymin,ymax (A): 35.16100 88.96500 zmin,zma (A): 17.17000 71.01400 x,y,z range (A): 40.99500 53.80400 53.84400 scale (grids/A): 1.983508 object centre (A): 12.68250 62.06300 44.09200 number of atom coordinates read : 2089 total number of charged atoms : 1960 net assigned charge : -1.699992 assigned positive charge : 305.4449 centred at (gu) : 87.89297 92.02041 87.04732 assigned negative charge : -307.1449 centred at (gu) : 87.87792 92.31568 86.30643 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20953 grid for indexing accessible points = 1.400000 m= 22294 mr = 42642 m= 3554 mr = 15493 m= 263 mr = 2054 m= 11 mr = 111 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1362 time to turn everything in is 0.5500000 number of dielectric boundary points 31755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15514 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) : 0.6611693 object centre at (A) : 12.68250 62.06300 44.09200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8844056E-02 5.7192314E-02 midg,1,midg; midg,igrid,midg 1.5991122E-02 -5.9838224E-02 1,midg,midg; igrid,midg,midg -1.3591972E-03 -1.0044775E-03 gauss-seidel spectral radius is 0.9987019 estimated iterations to convergence 220 setup time was (sec) 0.8300000 now iterating at: 17:10:32 rms-change max change #iterations 4.106408 172.1176 at 10iterations 1.949608 66.21239 at 20iterations 0.9226580 32.98729 at 30iterations 0.4404098 14.19863 at 40iterations 0.2087073 7.068560 at 50iterations 9.9648789E-02 3.347912 at 60iterations 4.7323007E-02 1.596136 at 70iterations 2.2549259E-02 0.7414206 at 80iterations 1.0790276E-02 0.3591146 at 90iterations 5.1338002E-03 0.1609985 at 100iterations 2.4405024E-03 7.7514648E-02 at 110iterations 1.1641475E-03 3.8261414E-02 at 120iterations finished qdiffx linear iterations at : 17:10:41 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 1.1641475E-03 3.8261414E-02 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.40000 DelPhi exited at 17:10:42 10.401u 0.472s 0:11.29 96.2% 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 Mon Oct 10 2011 at 17:10:42 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIZ 66 has a net charge of 0.2000 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIY 94 has a net charge of 0.2000 !!! WARNING: HIZ 116 has a net charge of 0.2000 !!! WARNING: HIZ 120 has a net charge of 0.2000 !!! WARNING: HIZ 126 has a net charge of 0.2000 !!! WARNING: HIZ 541 has a net charge of 0.2000 !!! WARNING: HIY 569 has a net charge of 0.2000 !!! WARNING: ZN6 632 has a net charge of 1.4000 !!! WARNING: ZN6 633 has a net charge of 1.4000 !!! WARNING: ZN6 639 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.975262 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): -7.815000 33.18000 ymin,ymax (A): 35.16100 88.96500 zmin,zma (A): 17.17000 71.01400 x,y,z range (A): 40.99500 53.80400 53.84400 scale (grids/A): 2.975262 object centre (A): 12.68250 62.06300 44.09200 number of atom coordinates read : 2089 total number of charged atoms : 1960 net assigned charge : -1.699992 assigned positive charge : 305.4449 centred at (gu) : 86.83942 93.03065 85.57108 assigned negative charge : -307.1449 centred at (gu) : 86.81680 93.47349 84.45964 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 152296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20953 grid for indexing accessible points = 1.400000 m= 72268 mr = 104296 m= 25431 mr = 56579 m= 6216 mr = 19773 m= 1044 mr = 4392 m= 91 mr = 634 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 4552 time to turn everything in is 1.450000 number of dielectric boundary points 71651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 15680 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) : 1.983508 object centre at (A) : 12.68250 62.06300 44.09200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3744552 0.9815226 midg,1,midg; midg,igrid,midg 0.3127497 -0.6258263 1,midg,midg; igrid,midg,midg 5.3913990E-04 -3.6141127E-02 gauss-seidel spectral radius is 0.9992799 estimated iterations to convergence 294 setup time was (sec) 1.780000 now iterating at: 17:10:44 rms-change max change #iterations 9.539783 377.9126 at 10iterations 5.643301 124.4068 at 20iterations 3.322107 72.61815 at 30iterations 1.953871 41.16870 at 40iterations 1.138229 25.50805 at 50iterations 0.6658928 14.25517 at 60iterations 0.3868515 7.390405 at 70iterations 0.2250964 4.589443 at 80iterations 0.1311942 2.501538 at 90iterations 7.6224446E-02 1.518452 at 100iterations 4.4168439E-02 0.8856564 at 110iterations 2.5595821E-02 0.5026932 at 120iterations 1.4849637E-02 0.3144474 at 130iterations 8.6257132E-03 0.1695328 at 140iterations 5.0092163E-03 9.4226837E-02 at 150iterations 2.9101549E-03 5.6007743E-02 at 160iterations 1.6932102E-03 3.0658722E-02 at 170iterations 9.8856282E-04 1.9256592E-02 at 180iterations finished qdiffx linear iterations at : 17:11:00 total time elapsed so far: 17.76000 # loops : 180 mean,max change (kT/e) : 9.8856282E-04 1.9256592E-02 energy calculations done at 17.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.93000 DelPhi exited at 17:11:01 17.931u 0.477s 0:18.85 97.6% 0+0k 0+0io 0pf+0w