Mon Oct 10 19:33:35 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 19:33:35 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: HIT 106 has a net charge of 0.5140 !!! WARNING: SEP 153 has a net charge of -0.4750 !!! WARNING: SER 360 has a net charge of 0.5000 !!! WARNING: CME 1 has a net charge of 0.1000 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: 0.5569462 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): -34.84400 21.56500 ymin,ymax (A): -16.48600 30.44400 zmin,zma (A): 10.62900 74.54900 x,y,z range (A): 56.40900 46.93000 63.92001 scale (grids/A): 0.5569462 object centre (A): -6.639501 6.979000 42.58900 number of atom coordinates read : 2999 total number of charged atoms : 2854 net assigned charge : 7.639026 assigned positive charge : 447.2752 centred at (gu) : 89.94074 90.98126 90.76720 assigned negative charge : -439.6375 centred at (gu) : 89.90398 90.85676 90.86079 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6029 nv = 96 ne = 84 npr = 60585 no. pairs analyzed = 60585 no. exposed pairs = 3703 no. arc points = 26398 no. surface atoms = 1250 nbur = 1749 mkacc time = 0.1500000 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= 232 mr = 3169 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.3400000 number of dielectric boundary points 3084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2612 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3529604E-09 -2.6151420E-10 midg,1,midg; midg,igrid,midg -4.0277792E-10 2.4439872E-09 1,midg,midg; igrid,midg,midg 3.6201889E-10 1.0637446E-09 gauss-seidel spectral radius is 0.9833725 estimated iterations to convergence 64 setup time was (sec) 0.6900000 now iterating at: 19:33:36 rms-change max change #iterations 8.1897713E-02 14.07070 at 10iterations 5.7315123E-03 0.9070053 at 20iterations 4.1007827E-04 6.4128399E-02 at 30iterations 3.2032858E-05 4.9743652E-03 at 40iterations 4.4076819E-06 1.2273788E-03 at 50iterations finished qdiffx linear iterations at : 19:33:41 total time elapsed so far: 4.940000 # loops : 50 mean,max change (kT/e) : 4.4076819E-06 1.2273788E-03 energy calculations done at 4.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.100000 DelPhi exited at 19:33:41 5.105u 0.379s 0:06.12 89.3% 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 19:33:41 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: HIT 106 has a net charge of 0.5140 !!! WARNING: SEP 153 has a net charge of -0.4750 !!! WARNING: SER 360 has a net charge of 0.5000 !!! WARNING: CME 1 has a net charge of 0.1000 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: 1.670838 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): -34.84400 21.56500 ymin,ymax (A): -16.48600 30.44400 zmin,zma (A): 10.62900 74.54900 x,y,z range (A): 56.40900 46.93000 63.92001 scale (grids/A): 1.670838 object centre (A): -6.639501 6.979000 42.58900 number of atom coordinates read : 2999 total number of charged atoms : 2854 net assigned charge : 7.639026 assigned positive charge : 447.2752 centred at (gu) : 89.82114 92.94313 92.30083 assigned negative charge : -439.6375 centred at (gu) : 89.71172 92.57003 92.58232 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26398 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19985 mr = 45785 m= 2084 mr = 13824 m= 57 mr = 1161 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3157 time to turn everything in is 0.5400000 number of dielectric boundary points 28396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 22009 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) : 0.5569462 object centre at (A) : -6.639501 6.979000 42.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3354851E-03 -2.3961614E-03 midg,1,midg; midg,igrid,midg -4.1981195E-03 1.1238972E-02 1,midg,midg; igrid,midg,midg 1.3531012E-02 1.7151702E-02 gauss-seidel spectral radius is 0.9982659 estimated iterations to convergence 191 setup time was (sec) 0.8200000 now iterating at: 19:33:51 rms-change max change #iterations 3.489674 156.8307 at 10iterations 1.472908 51.09328 at 20iterations 0.6253386 23.36210 at 30iterations 0.2661803 9.390519 at 40iterations 0.1135644 4.262726 at 50iterations 4.8222288E-02 1.838654 at 60iterations 2.0472107E-02 0.7052746 at 70iterations 8.7243263E-03 0.3543336 at 80iterations 3.7040464E-03 0.1292753 at 90iterations 1.5809110E-03 6.0279846E-02 at 100iterations 6.7107705E-04 2.4673462E-02 at 110iterations 2.8689567E-04 9.6759796E-03 at 120iterations finished qdiffx linear iterations at : 19:34:01 total time elapsed so far: 11.06000 # loops : 120 mean,max change (kT/e) : 2.8689567E-04 9.6759796E-03 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 19:34:02 11.227u 0.493s 0:20.72 56.5% 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 19:34:02 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: HIT 106 has a net charge of 0.5140 !!! WARNING: SEP 153 has a net charge of -0.4750 !!! WARNING: SER 360 has a net charge of 0.5000 !!! WARNING: CME 1 has a net charge of 0.1000 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: 2.506258 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): -34.84400 21.56500 ymin,ymax (A): -16.48600 30.44400 zmin,zma (A): 10.62900 74.54900 x,y,z range (A): 56.40900 46.93000 63.92001 scale (grids/A): 2.506258 object centre (A): -6.639501 6.979000 42.58900 number of atom coordinates read : 2999 total number of charged atoms : 2854 net assigned charge : 7.639026 assigned positive charge : 447.2752 centred at (gu) : 89.73148 94.41428 93.45110 assigned negative charge : -439.6375 centred at (gu) : 89.56759 93.85479 93.87343 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26398 grid for indexing accessible points = 1.400000 m= 69983 mr = 112033 m= 19378 mr = 55665 m= 3315 mr = 14691 m= 251 mr = 2358 m= 3 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 10433 time to turn everything in is 1.490000 number of dielectric boundary points 64036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 22802 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) : 1.670838 object centre at (A) : -6.639501 6.979000 42.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2182078 6.7096546E-02 midg,1,midg; midg,igrid,midg -6.5098815E-02 0.1182110 1,midg,midg; igrid,midg,midg 0.1695617 0.2980025 gauss-seidel spectral radius is 0.9991641 estimated iterations to convergence 273 setup time was (sec) 1.800000 now iterating at: 19:34:04 rms-change max change #iterations 8.815048 294.8861 at 10iterations 4.940897 114.4163 at 20iterations 2.751500 59.25156 at 30iterations 1.537632 34.81837 at 40iterations 0.8517975 24.64856 at 50iterations 0.4740130 11.04800 at 60iterations 0.2632000 5.648537 at 70iterations 0.1460086 3.011932 at 80iterations 8.0978066E-02 1.575130 at 90iterations 4.4916075E-02 0.8966146 at 100iterations 2.4922632E-02 0.5123100 at 110iterations 1.3818567E-02 0.2960377 at 120iterations 7.6609384E-03 0.1602783 at 130iterations 4.2482601E-03 8.4835052E-02 at 140iterations 2.3560107E-03 4.9187064E-02 at 150iterations 1.3050090E-03 2.7183533E-02 at 160iterations 7.2549481E-04 1.5774131E-02 at 170iterations 4.0410995E-04 8.7575912E-03 at 180iterations finished qdiffx linear iterations at : 19:34:21 total time elapsed so far: 18.38000 # loops : 180 mean,max change (kT/e) : 4.0410995E-04 8.7575912E-03 energy calculations done at 18.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 19:34:22 18.543u 0.497s 0:19.43 97.9% 0+0k 0+0io 0pf+0w