Sat Oct 8 18:58:04 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+sph.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 = amb.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 Sat Oct 8 2011 at 18:58:04 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! 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: ZN6 667 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6177445 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): -31.58100 17.51800 ymin,ymax (A): -23.62500 22.89300 zmin,zma (A): -12.68800 44.94100 x,y,z range (A): 49.09900 46.51800 57.62900 scale (grids/A): 0.6177445 object centre (A): -7.031501 -0.3660002 16.12650 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 88.46227 89.29729 89.78113 assigned negative charge : -388.8705 centred at (gu) : 88.35430 89.34074 89.67380 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6569 nv = 96 ne = 84 npr = 53805 no. pairs analyzed = 53805 no. exposed pairs = 3035 no. arc points = 21814 no. surface atoms = 1016 nbur = 1586 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3661 m= 0 mr = 54 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 196 time to turn everything in is 0.3400000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8042 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4377849E-09 9.6064383E-09 midg,1,midg; midg,igrid,midg 7.2100650E-09 6.8686601E-10 1,midg,midg; igrid,midg,midg -4.7777191E-09 7.2250601E-09 gauss-seidel spectral radius is 0.9864280 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 18:58:05 rms-change max change #iterations 0.1279076 21.06692 at 10iterations 1.1331712E-02 1.732883 at 20iterations 1.0557508E-03 0.1496639 at 30iterations 9.4993156E-05 1.3679504E-02 at 40iterations 8.7578446E-06 1.2922287E-03 at 50iterations finished qdiffx linear iterations at : 18:58:08 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 8.7578446E-06 1.2922287E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 18:58:09 4.159u 0.275s 0:04.73 93.4% 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 Sat Oct 8 2011 at 18:58:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! 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: ZN6 667 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.853234 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): -31.58100 17.51800 ymin,ymax (A): -23.62500 22.89300 zmin,zma (A): -12.68800 44.94100 x,y,z range (A): 49.09900 46.51800 57.62900 scale (grids/A): 1.853234 object centre (A): -7.031501 -0.3660002 16.12650 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 85.38637 87.89157 89.34326 assigned negative charge : -388.8705 centred at (gu) : 85.06275 88.02192 89.02099 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71135 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21814 grid for indexing accessible points = 1.400000 m= 24916 mr = 49775 m= 3620 mr = 18579 m= 196 mr = 2274 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 6577 time to turn everything in is 0.6200000 number of dielectric boundary points 29165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19299 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) : 0.6177445 object centre at (A) : -7.031501 -0.3660002 16.12650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4764809E-02 2.7024744E-02 midg,1,midg; midg,igrid,midg 1.3623596E-02 1.0231202E-03 1,midg,midg; igrid,midg,midg -4.1256314E-03 3.0604480E-02 gauss-seidel spectral radius is 0.9985585 estimated iterations to convergence 209 setup time was (sec) 0.9300000 now iterating at: 18:58:10 rms-change max change #iterations 4.006680 170.0526 at 10iterations 1.837570 62.07503 at 20iterations 0.8404861 29.18845 at 30iterations 0.3858138 13.36244 at 40iterations 0.1774659 5.850376 at 50iterations 8.1546776E-02 2.714507 at 60iterations 3.7427958E-02 1.265348 at 70iterations 1.7163137E-02 0.5440350 at 80iterations 7.8830682E-03 0.2551918 at 90iterations 3.6041297E-03 0.1162586 at 100iterations 1.6592885E-03 5.8555126E-02 at 110iterations 7.6070277E-04 2.2994995E-02 at 120iterations finished qdiffx linear iterations at : 18:58:19 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 7.6070277E-04 2.2994995E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 18:58:19 9.600u 0.311s 0:10.18 97.3% 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 Sat Oct 8 2011 at 18:58:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! 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: ZN6 667 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.779850 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): -31.58100 17.51800 ymin,ymax (A): -23.62500 22.89300 zmin,zma (A): -12.68800 44.94100 x,y,z range (A): 49.09900 46.51800 57.62900 scale (grids/A): 2.779850 object centre (A): -7.031501 -0.3660002 16.12650 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 83.07941 86.83724 89.01478 assigned negative charge : -388.8705 centred at (gu) : 82.59408 87.03278 88.53147 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 164490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21814 grid for indexing accessible points = 1.400000 m= 82721 mr = 120489 m= 28429 mr = 68327 m= 6319 mr = 22907 m= 848 mr = 4785 m= 43 mr = 568 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 21747 time to turn everything in is 1.580000 number of dielectric boundary points 65748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19695 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) : 1.853234 object centre at (A) : -7.031501 -0.3660002 16.12650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3565238E-02 0.3965942 midg,1,midg; midg,igrid,midg 0.1650621 -3.5191434E-03 1,midg,midg; igrid,midg,midg -1.5730094E-02 0.3808869 gauss-seidel spectral radius is 0.9992330 estimated iterations to convergence 285 setup time was (sec) 1.900000 now iterating at: 18:58:21 rms-change max change #iterations 9.491098 397.7014 at 10iterations 5.432486 113.7508 at 20iterations 3.094443 68.63208 at 30iterations 1.765542 37.66042 at 40iterations 1.005304 19.30900 at 50iterations 0.5714556 10.80491 at 60iterations 0.3248554 6.268536 at 70iterations 0.1843997 4.001911 at 80iterations 0.1049712 1.954189 at 90iterations 5.9601814E-02 1.218596 at 100iterations 3.3863895E-02 0.6210120 at 110iterations 1.9270629E-02 0.3620453 at 120iterations 1.0967907E-02 0.2038050 at 130iterations 6.2248413E-03 0.1233554 at 140iterations 3.5410977E-03 7.1331024E-02 at 150iterations 2.0105070E-03 3.6666870E-02 at 160iterations 1.1434248E-03 2.3185730E-02 at 170iterations 6.5096404E-04 1.4270782E-02 at 180iterations finished qdiffx linear iterations at : 18:58:35 total time elapsed so far: 15.77000 # loops : 180 mean,max change (kT/e) : 6.5096404E-04 1.4270782E-02 energy calculations done at 15.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 18:58:36 15.959u 0.334s 0:16.59 98.1% 0+0k 0+0io 0pf+0w