Sat Oct 8 19:34:29 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 19:34:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! 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: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 352 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6218883 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): -31.98600 17.56600 ymin,ymax (A): -23.18700 23.51000 zmin,zma (A): -12.35200 44.89300 x,y,z range (A): 49.55200 46.69700 57.24500 scale (grids/A): 0.6218883 object centre (A): -7.210000 0.1615000 16.27050 number of atom coordinates read : 2567 total number of charged atoms : 2444 net assigned charge : 4.000008 assigned positive charge : 389.4101 centred at (gu) : 88.50986 88.93231 89.77385 assigned negative charge : -385.4105 centred at (gu) : 88.43612 88.99663 89.62926 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6532 nv = 96 ne = 84 npr = 53131 no. pairs analyzed = 53131 no. exposed pairs = 2965 no. arc points = 20989 no. surface atoms = 1002 nbur = 1565 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3680 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2900000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2146 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8074 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1001192E-09 1.2701028E-08 midg,1,midg; midg,igrid,midg 9.9996047E-09 -7.7956003E-10 1,midg,midg; igrid,midg,midg -2.4624591E-09 6.1846701E-09 gauss-seidel spectral radius is 0.9866021 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 19:34:30 rms-change max change #iterations 0.1306121 18.63351 at 10iterations 1.2179967E-02 1.982073 at 20iterations 1.1323229E-03 0.1663971 at 30iterations 1.1104024E-04 1.5430450E-02 at 40iterations 1.0755597E-05 1.5163422E-03 at 50iterations finished qdiffx linear iterations at : 19:34:32 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.0755597E-05 1.5163422E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 19:34:33 3.078u 0.137s 0:03.55 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 8 2011 at 19:34:33 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! 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: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 352 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.865665 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): -31.98600 17.56600 ymin,ymax (A): -23.18700 23.51000 zmin,zma (A): -12.35200 44.89300 x,y,z range (A): 49.55200 46.69700 57.24500 scale (grids/A): 1.865665 object centre (A): -7.210000 0.1615000 16.27050 number of atom coordinates read : 2567 total number of charged atoms : 2444 net assigned charge : 4.000008 assigned positive charge : 389.4101 centred at (gu) : 85.52926 86.79647 89.32122 assigned negative charge : -385.4105 centred at (gu) : 85.30814 86.98973 88.88735 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20989 grid for indexing accessible points = 1.400000 m= 25443 mr = 50104 m= 3625 mr = 19057 m= 175 mr = 2255 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2210 time to turn everything in is 0.5000000 number of dielectric boundary points 28804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19217 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) : 0.6218883 object centre at (A) : -7.210000 0.1615000 16.27050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2492735E-02 2.5651604E-02 midg,1,midg; midg,igrid,midg 1.5336189E-02 1.6435721E-03 1,midg,midg; igrid,midg,midg -1.8459081E-03 3.2875806E-02 gauss-seidel spectral radius is 0.9985711 estimated iterations to convergence 210 setup time was (sec) 0.7700000 now iterating at: 19:34:34 rms-change max change #iterations 4.029786 159.7038 at 10iterations 1.858110 69.10495 at 20iterations 0.8532300 28.99581 at 30iterations 0.3926192 13.15046 at 40iterations 0.1816423 5.612763 at 50iterations 8.3398417E-02 2.624150 at 60iterations 3.8471442E-02 1.175584 at 70iterations 1.7741103E-02 0.7023163 at 80iterations 8.1514688E-03 0.2887459 at 90iterations 3.7617043E-03 0.1225052 at 100iterations 1.7323551E-03 5.3791046E-02 at 110iterations 7.9536252E-04 2.5331736E-02 at 120iterations finished qdiffx linear iterations at : 19:34:40 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 7.9536252E-04 2.5331736E-02 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.780000 DelPhi exited at 19:34:40 6.786u 0.151s 0:07.20 96.2% 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 19:34:40 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! 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: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 352 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.798497 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): -31.98600 17.56600 ymin,ymax (A): -23.18700 23.51000 zmin,zma (A): -12.35200 44.89300 x,y,z range (A): 49.55200 46.69700 57.24500 scale (grids/A): 2.798497 object centre (A): -7.210000 0.1615000 16.27050 number of atom coordinates read : 2567 total number of charged atoms : 2444 net assigned charge : 4.000008 assigned positive charge : 389.4101 centred at (gu) : 83.29385 85.19454 88.98167 assigned negative charge : -385.4105 centred at (gu) : 82.96208 85.48457 88.33105 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 164428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20989 grid for indexing accessible points = 1.400000 m= 83429 mr = 121209 m= 28925 mr = 69212 m= 6402 mr = 23356 m= 845 mr = 4813 m= 43 mr = 555 m= 0 mr = 12 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 7294 time to turn everything in is 1.200000 number of dielectric boundary points 64915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 19549 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) : 1.865665 object centre at (A) : -7.210000 0.1615000 16.27050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1022651 0.2609479 midg,1,midg; midg,igrid,midg 0.1902270 1.3936889E-02 1,midg,midg; igrid,midg,midg 2.2768311E-02 0.3834351 gauss-seidel spectral radius is 0.9992336 estimated iterations to convergence 285 setup time was (sec) 1.450000 now iterating at: 19:34:42 rms-change max change #iterations 9.457891 393.1119 at 10iterations 5.433708 123.2531 at 20iterations 3.108392 66.37593 at 30iterations 1.773415 33.37354 at 40iterations 1.011010 20.25198 at 50iterations 0.5753025 13.34689 at 60iterations 0.3274828 5.954592 at 70iterations 0.1865599 3.545911 at 80iterations 0.1061284 2.278355 at 90iterations 6.0538199E-02 1.137524 at 100iterations 3.4295961E-02 0.6371633 at 110iterations 1.9533126E-02 0.3354340 at 120iterations 1.1117169E-02 0.2185574 at 130iterations 6.3300305E-03 0.1202183 at 140iterations 3.6039120E-03 6.5265656E-02 at 150iterations 2.0511348E-03 4.4244766E-02 at 160iterations 1.1680109E-03 2.1476746E-02 at 170iterations 6.6671899E-04 1.3164520E-02 at 180iterations finished qdiffx linear iterations at : 19:34:52 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 6.6671899E-04 1.3164520E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 19:34:52 11.625u 0.185s 0:12.08 97.6% 0+0k 0+0io 0pf+0w