Sat Oct 15 15:19:57 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 Sat Oct 15 2011 at 15:19:57 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3339 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.5278218 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): 112.4780 170.0320 ymin,ymax (A): 18.07600 65.76400 zmin,zma (A): -10.50800 56.93900 x,y,z range (A): 57.55400 47.68800 67.44701 scale (grids/A): 0.5278218 object centre (A): 141.2550 41.92000 23.21550 number of atom coordinates read : 3339 total number of charged atoms : 3174 net assigned charge : -0.5489699 assigned positive charge : 516.6906 centred at (gu) : 90.21643 90.09391 87.88223 assigned negative charge : -517.2405 centred at (gu) : 90.32534 90.21714 87.80424 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5776 nv = 96 ne = 84 npr = 67632 no. pairs analyzed = 67632 no. exposed pairs = 3957 no. arc points = 27791 no. surface atoms = 1336 nbur = 2003 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 219 mr = 3024 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2837 ## 431 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3527344E-10 1.6645715E-10 midg,1,midg; midg,igrid,midg 4.4368390E-10 -4.9570370E-10 1,midg,midg; igrid,midg,midg 3.7979134E-10 -4.5229645E-10 gauss-seidel spectral radius is 0.9815280 estimated iterations to convergence 61 setup time was (sec) 0.4300000 now iterating at: 15:19:58 rms-change max change #iterations 6.9721401E-02 12.11104 at 10iterations 4.3974263E-03 0.8356676 at 20iterations 2.9656338E-04 5.5931091E-02 at 30iterations 3.4937526E-05 8.2206726E-03 at 40iterations 6.6599214E-06 1.7280579E-03 at 50iterations finished qdiffx linear iterations at : 15:20:01 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 6.6599214E-06 1.7280579E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 15:20:01 3.564u 0.213s 0:04.18 90.1% 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 Sat Oct 15 2011 at 15:20:01 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3339 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 1.583465 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): 112.4780 170.0320 ymin,ymax (A): 18.07600 65.76400 zmin,zma (A): -10.50800 56.93900 x,y,z range (A): 57.55400 47.68800 67.44701 scale (grids/A): 1.583465 object centre (A): 141.2550 41.92000 23.21550 number of atom coordinates read : 3339 total number of charged atoms : 3174 net assigned charge : -0.5489699 assigned positive charge : 516.6906 centred at (gu) : 90.64833 90.28078 83.64592 assigned negative charge : -517.2405 centred at (gu) : 90.97560 90.65105 83.41227 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20036 mr = 43674 m= 1865 mr = 13932 m= 45 mr = 853 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1306 time to turn everything in is 0.3300000 number of dielectric boundary points 27569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 399 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 24078 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) : 0.5278218 object centre at (A) : 141.2550 41.92000 23.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1962342E-02 1.2156595E-02 midg,1,midg; midg,igrid,midg 1.8979703E-03 -5.2428432E-03 1,midg,midg; igrid,midg,midg 1.6140716E-02 1.0823244E-03 gauss-seidel spectral radius is 0.9980889 estimated iterations to convergence 182 setup time was (sec) 0.5400000 now iterating at: 15:20:02 rms-change max change #iterations 3.398267 162.2022 at 10iterations 1.387048 53.13204 at 20iterations 0.5646855 20.74698 at 30iterations 0.2305608 8.625994 at 40iterations 9.3899496E-02 3.871523 at 50iterations 3.8407188E-02 1.382826 at 60iterations 1.5671782E-02 0.5762240 at 70iterations 6.3962522E-03 0.2457237 at 80iterations 2.6349763E-03 0.1144447 at 90iterations 1.0861580E-03 3.8688660E-02 at 100iterations 4.4850906E-04 1.5821457E-02 at 110iterations 1.9032789E-04 6.9732666E-03 at 120iterations finished qdiffx linear iterations at : 15:20:09 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.9032789E-04 6.9732666E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 15:20:10 7.940u 0.239s 0:08.45 96.6% 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 15 2011 at 15:20:10 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3339 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.375198 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): 112.4780 170.0320 ymin,ymax (A): 18.07600 65.76400 zmin,zma (A): -10.50800 56.93900 x,y,z range (A): 57.55400 47.68800 67.44701 scale (grids/A): 2.375198 object centre (A): 141.2550 41.92000 23.21550 number of atom coordinates read : 3339 total number of charged atoms : 3174 net assigned charge : -0.5489699 assigned positive charge : 516.6906 centred at (gu) : 90.97218 90.42101 80.46874 assigned negative charge : -517.2405 centred at (gu) : 91.46331 90.97642 80.11833 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 148785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 69363 mr = 106554 m= 19759 mr = 55458 m= 2840 mr = 14750 m= 142 mr = 1732 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4431 time to turn everything in is 0.8000000 number of dielectric boundary points 62351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 25348 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) : 1.583465 object centre at (A) : 141.2550 41.92000 23.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0842644E-02 0.2579740 midg,1,midg; midg,igrid,midg 2.5705120E-02 -4.1656356E-02 1,midg,midg; igrid,midg,midg 0.2370122 3.3159006E-02 gauss-seidel spectral radius is 0.9991085 estimated iterations to convergence 265 setup time was (sec) 1.060000 now iterating at: 15:20:11 rms-change max change #iterations 8.825621 304.1028 at 10iterations 4.874458 122.9743 at 20iterations 2.674396 64.30251 at 30iterations 1.463186 37.49632 at 40iterations 0.7996327 20.88069 at 50iterations 0.4371360 9.709003 at 60iterations 0.2378112 5.298991 at 70iterations 0.1294820 2.700596 at 80iterations 7.0366107E-02 1.475821 at 90iterations 3.8297176E-02 0.8405857 at 100iterations 2.0813998E-02 0.4330387 at 110iterations 1.1319083E-02 0.2330222 at 120iterations 6.1462396E-03 0.1275921 at 130iterations 3.3519408E-03 7.2116852E-02 at 140iterations 1.8231152E-03 3.9387703E-02 at 150iterations 9.9302363E-04 1.9406557E-02 at 160iterations 5.4032210E-04 1.1428833E-02 at 170iterations 2.9615249E-04 6.6301823E-03 at 180iterations finished qdiffx linear iterations at : 15:20:22 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 2.9615249E-04 6.6301823E-03 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 15:20:23 12.768u 0.245s 0:13.38 97.1% 0+0k 0+0io 0pf+0w