Mon Oct 10 14:01:33 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 Mon Oct 10 2011 at 14:01:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 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: 0.6484990 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): 1.139000 53.26500 ymin,ymax (A): 8.547999 51.05700 zmin,zma (A): -6.293000 48.60300 x,y,z range (A): 52.12600 42.50900 54.89600 scale (grids/A): 0.6484990 object centre (A): 27.20200 29.80250 21.15500 number of atom coordinates read : 2220 total number of charged atoms : 2086 net assigned charge : 8.500019 assigned positive charge : 321.1898 centred at (gu) : 89.24363 90.65725 88.99038 assigned negative charge : -312.6902 centred at (gu) : 89.26410 90.56122 88.94423 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6512 nv = 96 ne = 84 npr = 44133 no. pairs analyzed = 44133 no. exposed pairs = 2922 no. arc points = 20969 no. surface atoms = 977 nbur = 1243 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3368 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2700000 number of dielectric boundary points 3455 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2080 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2481236E-08 1.7141318E-08 midg,1,midg; midg,igrid,midg 3.7889580E-09 3.0861827E-08 1,midg,midg; igrid,midg,midg 2.1147763E-08 1.1394095E-08 gauss-seidel spectral radius is 0.9876547 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 14:01:34 rms-change max change #iterations 0.1353884 20.64021 at 10iterations 1.3736859E-02 2.324780 at 20iterations 1.3795225E-03 0.2069359 at 30iterations 1.4705549E-04 2.5527954E-02 at 40iterations 1.5275189E-05 2.4232864E-03 at 50iterations finished qdiffx linear iterations at : 14:01:36 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.5275189E-05 2.4232864E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 14:01:37 3.252u 0.181s 0:03.83 89.5% 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 14:01:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 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: 1.945497 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): 1.139000 53.26500 ymin,ymax (A): 8.547999 51.05700 zmin,zma (A): -6.293000 48.60300 x,y,z range (A): 52.12600 42.50900 54.89600 scale (grids/A): 1.945497 object centre (A): 27.20200 29.80250 21.15500 number of atom coordinates read : 2220 total number of charged atoms : 2086 net assigned charge : 8.500019 assigned positive charge : 321.1898 centred at (gu) : 87.73038 91.97168 86.97077 assigned negative charge : -312.6902 centred at (gu) : 87.79243 91.68375 86.83286 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20969 grid for indexing accessible points = 1.400000 m= 24845 mr = 46122 m= 4172 mr = 17847 m= 293 mr = 2575 m= 4 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1901 time to turn everything in is 0.5100000 number of dielectric boundary points 31764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 16427 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) : 0.6484990 object centre at (A) : 27.20200 29.80250 21.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6083362E-02 5.2503061E-02 midg,1,midg; midg,igrid,midg -4.0168539E-03 2.3603203E-02 1,midg,midg; igrid,midg,midg 5.1817078E-02 4.1987341E-02 gauss-seidel spectral radius is 0.9986623 estimated iterations to convergence 217 setup time was (sec) 0.7900000 now iterating at: 14:01:38 rms-change max change #iterations 3.930521 191.2395 at 10iterations 1.850582 76.89273 at 20iterations 0.8688012 29.88104 at 30iterations 0.4100421 14.20512 at 40iterations 0.1935296 5.627270 at 50iterations 9.0959780E-02 2.983773 at 60iterations 4.2796619E-02 1.364244 at 70iterations 2.0153824E-02 0.6953256 at 80iterations 9.5080994E-03 0.3186340 at 90iterations 4.4813668E-03 0.1483955 at 100iterations 2.1152960E-03 6.6716194E-02 at 110iterations 9.9842576E-04 3.2436371E-02 at 120iterations finished qdiffx linear iterations at : 14:01:44 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 9.9842576E-04 3.2436371E-02 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 14:01:45 7.416u 0.245s 0:08.42 90.8% 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 14:01:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 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: 2.918246 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): 1.139000 53.26500 ymin,ymax (A): 8.547999 51.05700 zmin,zma (A): -6.293000 48.60300 x,y,z range (A): 52.12600 42.50900 54.89600 scale (grids/A): 2.918246 object centre (A): 27.20200 29.80250 21.15500 number of atom coordinates read : 2220 total number of charged atoms : 2086 net assigned charge : 8.500019 assigned positive charge : 321.1898 centred at (gu) : 86.59558 92.95756 85.45628 assigned negative charge : -312.6902 centred at (gu) : 86.68867 92.52558 85.24928 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 159449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20969 grid for indexing accessible points = 1.400000 m= 79401 mr = 112031 m= 29525 mr = 63642 m= 7577 mr = 23427 m= 1305 mr = 5684 m= 87 mr = 879 m= 0 mr = 48 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 6661 time to turn everything in is 1.220000 number of dielectric boundary points 71633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 16688 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) : 1.945497 object centre at (A) : 27.20200 29.80250 21.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2330069 0.8074927 midg,1,midg; midg,igrid,midg -3.0256817E-02 0.2341599 1,midg,midg; igrid,midg,midg 0.4862132 0.5448940 gauss-seidel spectral radius is 0.9992691 estimated iterations to convergence 292 setup time was (sec) 1.500000 now iterating at: 14:01:47 rms-change max change #iterations 9.336990 410.4897 at 10iterations 5.500597 144.9927 at 20iterations 3.212131 87.32880 at 30iterations 1.866257 39.05227 at 40iterations 1.083193 22.53961 at 50iterations 0.6268454 13.41296 at 60iterations 0.3631869 8.551954 at 70iterations 0.2107992 4.384706 at 80iterations 0.1211171 2.349985 at 90iterations 7.0121653E-02 1.295883 at 100iterations 4.0484309E-02 0.8617401 at 110iterations 2.3397218E-02 0.4295273 at 120iterations 1.3519751E-02 0.2751389 at 130iterations 7.7952379E-03 0.1436243 at 140iterations 4.4876332E-03 8.8563919E-02 at 150iterations 2.5927713E-03 5.3909302E-02 at 160iterations 1.4951424E-03 2.8594971E-02 at 170iterations 8.6461077E-04 1.6983032E-02 at 180iterations finished qdiffx linear iterations at : 14:01:57 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 8.6461077E-04 1.6983032E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 14:01:58 11.895u 0.231s 0:12.63 95.9% 0+0k 0+0io 0pf+0w