Mon Oct 10 13:58:52 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 13:58:52 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN5 556 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: 0.6431682 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): -31.43600 18.07800 ymin,ymax (A): -23.90300 23.18600 zmin,zma (A): -11.34000 44.01100 x,y,z range (A): 49.51400 47.08900 55.35100 scale (grids/A): 0.6431682 object centre (A): -6.679001 -0.3585005 16.33550 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 5.406007 assigned positive charge : 396.1270 centred at (gu) : 88.25957 89.23201 89.63474 assigned negative charge : -390.7216 centred at (gu) : 88.18000 89.27947 89.47388 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7088 nv = 96 ne = 84 npr = 55302 no. pairs analyzed = 55302 no. exposed pairs = 3018 no. arc points = 21754 no. surface atoms = 1010 nbur = 1609 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 3979 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 241 time to turn everything in is 0.3600000 number of dielectric boundary points 3421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3060005E-08 2.6809511E-08 midg,1,midg; midg,igrid,midg 1.7473196E-08 2.4021287E-09 1,midg,midg; igrid,midg,midg -2.3027862E-09 1.3114511E-08 gauss-seidel spectral radius is 0.9874712 estimated iterations to convergence 73 setup time was (sec) 0.6500000 now iterating at: 13:58:53 rms-change max change #iterations 0.1506503 22.18971 at 10iterations 1.4922439E-02 2.106108 at 20iterations 1.5374433E-03 0.2272720 at 30iterations 1.5232482E-04 1.9258499E-02 at 40iterations 1.5427193E-05 2.2430420E-03 at 50iterations finished qdiffx linear iterations at : 13:58:56 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.5427193E-05 2.2430420E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 13:58:57 4.118u 0.226s 0:04.90 88.3% 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 Mon Oct 10 2011 at 13:58:57 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN5 556 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: 1.929504 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): -31.43600 18.07800 ymin,ymax (A): -23.90300 23.18600 zmin,zma (A): -11.34000 44.01100 x,y,z range (A): 49.51400 47.08900 55.35100 scale (grids/A): 1.929504 object centre (A): -6.679001 -0.3585005 16.33550 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 5.406007 assigned positive charge : 396.1270 centred at (gu) : 84.77850 87.69558 88.90367 assigned negative charge : -390.7216 centred at (gu) : 84.53990 87.83826 88.42152 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21754 grid for indexing accessible points = 1.400000 m= 27731 mr = 53874 m= 4413 mr = 20710 m= 279 mr = 2819 m= 4 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 6349 time to turn everything in is 0.6800000 number of dielectric boundary points 31387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 19508 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) : 0.6431682 object centre at (A) : -6.679001 -0.3585005 16.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0467980E-02 3.9682839E-02 midg,1,midg; midg,igrid,midg 1.6587362E-02 2.2614193E-03 1,midg,midg; igrid,midg,midg -2.2695616E-03 3.9365847E-02 gauss-seidel spectral radius is 0.9986643 estimated iterations to convergence 217 setup time was (sec) 0.9900000 now iterating at: 13:58:58 rms-change max change #iterations 4.347247 165.1118 at 10iterations 2.054139 68.67178 at 20iterations 0.9713493 32.57746 at 30iterations 0.4597865 13.60102 at 40iterations 0.2161432 7.525576 at 50iterations 0.1020384 3.273269 at 60iterations 4.8371822E-02 1.627059 at 70iterations 2.2774011E-02 0.7385926 at 80iterations 1.0761620E-02 0.3247871 at 90iterations 5.0945375E-03 0.1715736 at 100iterations 2.3994497E-03 7.8445435E-02 at 110iterations 1.1365114E-03 3.1565666E-02 at 120iterations finished qdiffx linear iterations at : 13:59:06 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.1365114E-03 3.1565666E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 13:59:07 9.460u 0.274s 0:10.09 96.4% 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 Mon Oct 10 2011 at 13:59:07 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN5 556 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: 2.894257 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): -31.43600 18.07800 ymin,ymax (A): -23.90300 23.18600 zmin,zma (A): -11.34000 44.01100 x,y,z range (A): 49.51400 47.08900 55.35100 scale (grids/A): 2.894257 object centre (A): -6.679001 -0.3585005 16.33550 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 5.406007 assigned positive charge : 396.1270 centred at (gu) : 82.16770 86.54336 88.35540 assigned negative charge : -390.7216 centred at (gu) : 81.80984 86.75726 87.63223 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 176618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21754 grid for indexing accessible points = 1.400000 m= 89731 mr = 129651 m= 32370 mr = 74418 m= 8040 mr = 26206 m= 1247 mr = 6170 m= 86 mr = 881 m= 6 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 21151 time to turn everything in is 1.740000 number of dielectric boundary points 70722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 19799 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) : 1.929504 object centre at (A) : -6.679001 -0.3585005 16.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1671574 0.3894591 midg,1,midg; midg,igrid,midg 0.1863442 1.3980233E-02 1,midg,midg; igrid,midg,midg -2.5405852E-02 0.4602289 gauss-seidel spectral radius is 0.9992595 estimated iterations to convergence 290 setup time was (sec) 2.060000 now iterating at: 13:59:09 rms-change max change #iterations 10.00265 561.2200 at 10iterations 5.785547 114.5724 at 20iterations 3.323982 60.57769 at 30iterations 1.906304 34.34465 at 40iterations 1.096170 20.34006 at 50iterations 0.6291803 11.77579 at 60iterations 0.3613028 6.482075 at 70iterations 0.2071545 3.877241 at 80iterations 0.1187653 2.143589 at 90iterations 6.8231955E-02 1.180952 at 100iterations 3.9112907E-02 0.6854000 at 110iterations 2.2467509E-02 0.4370451 at 120iterations 1.2864790E-02 0.2665405 at 130iterations 7.3964787E-03 0.1371698 at 140iterations 4.2368094E-03 7.3116302E-02 at 150iterations 2.4291042E-03 4.2419434E-02 at 160iterations 1.3952330E-03 2.2735596E-02 at 170iterations 8.0172066E-04 1.3574600E-02 at 180iterations finished qdiffx linear iterations at : 13:59:23 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 8.0172066E-04 1.3574600E-02 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.88000 DelPhi exited at 13:59:24 15.887u 0.316s 0:17.10 94.6% 0+0k 0+0io 0pf+0w