Sat Oct 8 16:54:25 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+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 16:54:25 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3707 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5554689 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): 15.40000 79.17000 ymin,ymax (A): 120.4160 184.5060 zmin,zma (A): -1.404000 59.94400 x,y,z range (A): 63.77000 64.09000 61.34800 scale (grids/A): 0.5554689 object centre (A): 47.28500 152.4610 29.27000 number of atom coordinates read : 3707 total number of charged atoms : 3492 net assigned charge : -0.4999657 assigned positive charge : 552.5337 centred at (gu) : 91.17727 91.38215 88.17236 assigned negative charge : -553.0351 centred at (gu) : 91.13871 91.20860 88.11667 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7557 nv = 96 ne = 84 npr = 73982 no. pairs analyzed = 73982 no. exposed pairs = 4814 no. arc points = 33958 no. surface atoms = 1605 nbur = 2102 mkacc time = 0.1900000 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 = 1.540000 m= 325 mr = 3905 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3289 ## 381 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1344994E-09 3.6791398E-10 midg,1,midg; midg,igrid,midg -1.5152775E-09 2.6968889E-09 1,midg,midg; igrid,midg,midg -3.8727196E-10 5.1049509E-10 gauss-seidel spectral radius is 0.9833475 estimated iterations to convergence 64 setup time was (sec) 0.6800000 now iterating at: 16:54:26 rms-change max change #iterations 9.0854101E-02 15.68731 at 10iterations 6.4024576E-03 1.168628 at 20iterations 5.7696912E-04 0.1005402 at 30iterations 1.1569481E-04 2.4345398E-02 at 40iterations 3.2350785E-05 6.9656372E-03 at 50iterations finished qdiffx linear iterations at : 16:54:30 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 3.2350785E-05 6.9656372E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 16:54:30 4.657u 0.386s 0:05.37 93.6% 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 8 2011 at 16:54:30 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3707 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.666407 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): 15.40000 79.17000 ymin,ymax (A): 120.4160 184.5060 zmin,zma (A): -1.404000 59.94400 x,y,z range (A): 63.77000 64.09000 61.34800 scale (grids/A): 1.666407 object centre (A): 47.28500 152.4610 29.27000 number of atom coordinates read : 3707 total number of charged atoms : 3492 net assigned charge : -0.4999657 assigned positive charge : 552.5337 centred at (gu) : 93.53116 94.14571 84.51609 assigned negative charge : -553.0351 centred at (gu) : 93.41579 93.62560 84.34991 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33958 grid for indexing accessible points = 1.400000 m= 26326 mr = 56300 m= 3099 mr = 18048 m= 113 mr = 1642 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 37001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 26865 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) : 0.5554689 object centre at (A) : 47.28500 152.4610 29.27000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0771995E-02 1.3982036E-02 midg,1,midg; midg,igrid,midg -6.7988210E-03 3.6180224E-02 1,midg,midg; igrid,midg,midg -1.0441288E-02 -1.9452712E-02 gauss-seidel spectral radius is 0.9983427 estimated iterations to convergence 195 setup time was (sec) 1.000000 now iterating at: 16:54:32 rms-change max change #iterations 3.914113 242.1976 at 10iterations 1.693743 84.89816 at 20iterations 0.7294657 27.44047 at 30iterations 0.3152779 12.87596 at 40iterations 0.1374591 5.726280 at 50iterations 5.9190229E-02 2.025431 at 60iterations 2.5683867E-02 0.7475137 at 70iterations 1.1155355E-02 0.3665094 at 80iterations 4.8689456E-03 0.1566229 at 90iterations 2.1169069E-03 7.0108414E-02 at 100iterations 9.3081553E-04 2.7969360E-02 at 110iterations 4.1360300E-04 1.3332367E-02 at 120iterations finished qdiffx linear iterations at : 16:54:42 total time elapsed so far: 11.51000 # loops : 120 mean,max change (kT/e) : 4.1360300E-04 1.3332367E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 16:54:43 11.669u 0.440s 0:12.42 97.4% 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 16:54:43 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3707 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 2.499610 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): 15.40000 79.17000 ymin,ymax (A): 120.4160 184.5060 zmin,zma (A): -1.404000 59.94400 x,y,z range (A): 63.77000 64.09000 61.34800 scale (grids/A): 2.499610 object centre (A): 47.28500 152.4610 29.27000 number of atom coordinates read : 3707 total number of charged atoms : 3492 net assigned charge : -0.4999657 assigned positive charge : 552.5337 centred at (gu) : 95.29671 96.21833 81.77380 assigned negative charge : -553.0351 centred at (gu) : 95.12354 95.43825 81.52480 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 194379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33958 grid for indexing accessible points = 1.400000 m= 89666 mr = 138413 m= 26845 mr = 70644 m= 5041 mr = 20136 m= 452 mr = 3452 m= 8 mr = 219 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.700000 number of dielectric boundary points 83527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 27909 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) : 1.666407 object centre at (A) : 47.28500 152.4610 29.27000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2308529 0.2574395 midg,1,midg; midg,igrid,midg -6.7443714E-02 0.5825552 1,midg,midg; igrid,midg,midg -0.1515005 -0.3544326 gauss-seidel spectral radius is 0.9992019 estimated iterations to convergence 279 setup time was (sec) 2.020000 now iterating at: 16:54:45 rms-change max change #iterations 10.13735 393.3616 at 10iterations 5.869981 141.5356 at 20iterations 3.384130 87.86296 at 30iterations 1.932151 45.12662 at 40iterations 1.101081 22.54394 at 50iterations 0.6245537 12.94780 at 60iterations 0.3535943 7.097376 at 70iterations 0.1998581 3.994999 at 80iterations 0.1128673 2.244897 at 90iterations 6.3601434E-02 1.272367 at 100iterations 3.5883766E-02 0.7456479 at 110iterations 2.0163536E-02 0.3909225 at 120iterations 1.1389988E-02 0.2135544 at 130iterations 6.4158719E-03 0.1203489 at 140iterations 3.6077460E-03 6.7962646E-02 at 150iterations 2.0347417E-03 3.7647247E-02 at 160iterations 1.1518346E-03 2.2619247E-02 at 170iterations 6.5013609E-04 1.1703491E-02 at 180iterations finished qdiffx linear iterations at : 16:55:02 total time elapsed so far: 18.87000 # loops : 180 mean,max change (kT/e) : 6.5013609E-04 1.1703491E-02 energy calculations done at 18.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.04000 DelPhi exited at 16:55:02 19.042u 0.491s 0:19.81 98.5% 0+0k 0+0io 0pf+0w