Sat Oct 8 16:55:03 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 8 2011 at 16:55:03 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: 384 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: 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 : 554.1337 centred at (gu) : 91.17741 91.39381 88.18172 assigned negative charge : -554.6350 centred at (gu) : 91.14027 91.21716 88.12516 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 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 = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 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 0.5500000 number of grid points assigned charge 9624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1517859E-09 3.7602696E-10 midg,1,midg; midg,igrid,midg -1.5423186E-09 2.7612528E-09 1,midg,midg; igrid,midg,midg -3.7612807E-10 4.8975690E-10 gauss-seidel spectral radius is 0.9833475 estimated iterations to convergence 64 setup time was (sec) 0.7100000 now iterating at: 16:55:04 rms-change max change #iterations 9.1994934E-02 15.68731 at 10iterations 6.4802649E-03 1.163153 at 20iterations 5.5610278E-04 9.5046997E-02 at 30iterations 1.0591783E-04 2.2300720E-02 at 40iterations 2.9340397E-05 6.3438416E-03 at 50iterations finished qdiffx linear iterations at : 16:55:08 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 2.9340397E-05 6.3438416E-03 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.820000 DelPhi exited at 16:55:08 4.824u 0.395s 0:05.51 94.5% 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 Sat Oct 8 2011 at 16:55:08 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: 384 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 : 554.1337 centred at (gu) : 93.53160 94.18068 84.54409 assigned negative charge : -554.6350 centred at (gu) : 93.42044 93.65126 84.37540 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 0.7000000 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 0.8700000 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 -1.0955565E-02 1.3783981E-02 midg,1,midg; midg,igrid,midg -7.0188092E-03 3.6855195E-02 1,midg,midg; igrid,midg,midg -1.0406612E-02 -1.9678980E-02 gauss-seidel spectral radius is 0.9983427 estimated iterations to convergence 195 setup time was (sec) 1.060000 now iterating at: 16:55:10 rms-change max change #iterations 3.928983 242.1976 at 10iterations 1.700378 84.89815 at 20iterations 0.7323104 27.44045 at 30iterations 0.3165631 12.87597 at 40iterations 0.1379431 5.726261 at 50iterations 5.9421092E-02 2.036425 at 60iterations 2.5774490E-02 0.7439165 at 70iterations 1.1193885E-02 0.3687286 at 80iterations 4.8829331E-03 0.1555815 at 90iterations 2.1206604E-03 6.9124222E-02 at 100iterations 9.3093334E-04 2.7512550E-02 at 110iterations 4.1219342E-04 1.3028145E-02 at 120iterations finished qdiffx linear iterations at : 16:55:19 total time elapsed so far: 10.69000 # loops : 120 mean,max change (kT/e) : 4.1219342E-04 1.3028145E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 16:55:20 10.861u 0.424s 0:11.58 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 16:55:20 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: 384 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: 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 : 554.1337 centred at (gu) : 95.29737 96.27078 81.81583 assigned negative charge : -554.6350 centred at (gu) : 95.13050 95.47673 81.56302 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 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 = 1.040000 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 1.840000 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 -0.2334949 0.2542415 midg,1,midg; midg,igrid,midg -7.0541151E-02 0.5900536 1,midg,midg; igrid,midg,midg -0.1505467 -0.3578102 gauss-seidel spectral radius is 0.9992019 estimated iterations to convergence 279 setup time was (sec) 2.050000 now iterating at: 16:55:22 rms-change max change #iterations 10.16873 393.3616 at 10iterations 5.886284 141.5356 at 20iterations 3.393374 87.78830 at 30iterations 1.937351 45.12666 at 40iterations 1.103933 22.54393 at 50iterations 0.6259540 13.17216 at 60iterations 0.3544654 7.095793 at 70iterations 0.2003258 4.037050 at 80iterations 0.1131116 2.267562 at 90iterations 6.3738674E-02 1.271248 at 100iterations 3.5963923E-02 0.7474437 at 110iterations 2.0204941E-02 0.3907356 at 120iterations 1.1413096E-02 0.2149429 at 130iterations 6.4283293E-03 0.1218758 at 140iterations 3.6139837E-03 6.8489075E-02 at 150iterations 2.0373825E-03 3.7384033E-02 at 160iterations 1.1522552E-03 2.2634506E-02 at 170iterations 6.4968574E-04 1.1558533E-02 at 180iterations finished qdiffx linear iterations at : 16:55:39 total time elapsed so far: 19.00000 # loops : 180 mean,max change (kT/e) : 6.4968574E-04 1.1558533E-02 energy calculations done at 19.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.16000 DelPhi exited at 16:55:40 19.163u 0.464s 0:19.91 98.5% 0+0k 0+0io 0pf+0w