Mon Oct 10 17:05:33 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 17:05:33 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIT 128 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6087239 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): 16.12400 71.54601 ymin,ymax (A): -37.35600 8.314000 zmin,zma (A): -31.09400 27.38900 x,y,z range (A): 55.42200 45.67000 58.48300 scale (grids/A): 0.6087239 object centre (A): 43.83500 -14.52100 -1.852500 number of atom coordinates read : 2603 total number of charged atoms : 2465 net assigned charge : 3.014012 assigned positive charge : 392.3167 centred at (gu) : 91.28738 89.34782 89.03719 assigned negative charge : -389.3035 centred at (gu) : 91.26585 89.45970 89.11806 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6550 nv = 96 ne = 84 npr = 52037 no. pairs analyzed = 52037 no. exposed pairs = 3439 no. arc points = 24048 no. surface atoms = 1158 nbur = 1445 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 3437 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2000000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2434 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7503927E-09 -1.8139785E-09 midg,1,midg; midg,igrid,midg 7.9698665E-09 -3.2538556E-09 1,midg,midg; igrid,midg,midg 4.5557527E-10 3.5102654E-09 gauss-seidel spectral radius is 0.9860357 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 17:05:34 rms-change max change #iterations 0.1134609 17.69496 at 10iterations 1.0150091E-02 1.412476 at 20iterations 9.0426835E-04 0.1447105 at 30iterations 9.7076088E-05 1.6830444E-02 at 40iterations 1.5269212E-05 3.2329559E-03 at 50iterations finished qdiffx linear iterations at : 17:05:37 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.5269212E-05 3.2329559E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:05:37 3.439u 0.195s 0:03.99 90.7% 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 17:05:37 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIT 128 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.826172 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): 16.12400 71.54601 ymin,ymax (A): -37.35600 8.314000 zmin,zma (A): -31.09400 27.38900 x,y,z range (A): 55.42200 45.67000 58.48300 scale (grids/A): 1.826172 object centre (A): 43.83500 -14.52100 -1.852500 number of atom coordinates read : 2603 total number of charged atoms : 2465 net assigned charge : 3.014012 assigned positive charge : 392.3167 centred at (gu) : 93.86153 88.04299 87.11112 assigned negative charge : -389.3035 centred at (gu) : 93.79732 88.37897 87.35361 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 23391 mr = 47841 m= 2995 mr = 16488 m= 143 mr = 1684 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.3400000 number of dielectric boundary points 31336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19313 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) : 0.6087239 object centre at (A) : 43.83500 -14.52100 -1.852500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2939965E-03 -1.8890150E-02 midg,1,midg; midg,igrid,midg 1.7826742E-02 -4.4905557E-03 1,midg,midg; igrid,midg,midg 2.2322014E-02 2.1029646E-02 gauss-seidel spectral radius is 0.9985238 estimated iterations to convergence 206 setup time was (sec) 0.5600000 now iterating at: 17:05:38 rms-change max change #iterations 3.920579 201.8004 at 10iterations 1.774217 62.47813 at 20iterations 0.8061342 28.42135 at 30iterations 0.3652413 11.70582 at 40iterations 0.1657494 6.141945 at 50iterations 7.5398333E-02 2.365561 at 60iterations 3.4222160E-02 1.136833 at 70iterations 1.5556785E-02 0.5512896 at 80iterations 7.0818816E-03 0.2281952 at 90iterations 3.2054665E-03 0.1115036 at 100iterations 1.4598725E-03 4.7042847E-02 at 110iterations 6.6199264E-04 2.1847725E-02 at 120iterations finished qdiffx linear iterations at : 17:05:45 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 6.6199264E-04 2.1847725E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 17:05:45 7.785u 0.229s 0:08.33 96.0% 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 17:05:45 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIT 128 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.739258 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): 16.12400 71.54601 ymin,ymax (A): -37.35600 8.314000 zmin,zma (A): -31.09400 27.38900 x,y,z range (A): 55.42200 45.67000 58.48300 scale (grids/A): 2.739258 object centre (A): 43.83500 -14.52100 -1.852500 number of atom coordinates read : 2603 total number of charged atoms : 2465 net assigned charge : 3.014012 assigned positive charge : 392.3167 centred at (gu) : 95.79205 87.06437 85.66652 assigned negative charge : -389.3035 centred at (gu) : 95.69594 87.56829 86.03038 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 164305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 78205 mr = 116983 m= 24889 mr = 62323 m= 4892 mr = 19128 m= 521 mr = 3444 m= 27 mr = 266 m= 0 mr = 7 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 0.8700000 number of dielectric boundary points 70688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19715 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) : 1.826172 object centre at (A) : 43.83500 -14.52100 -1.852500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6548535E-02 9.3602300E-02 midg,1,midg; midg,igrid,midg 0.2333872 -2.1160319E-02 1,midg,midg; igrid,midg,midg 0.2026279 0.2374044 gauss-seidel spectral radius is 0.9992411 estimated iterations to convergence 287 setup time was (sec) 1.110000 now iterating at: 17:05:47 rms-change max change #iterations 9.449436 371.0211 at 10iterations 5.441978 122.3492 at 20iterations 3.121124 75.03139 at 30iterations 1.786723 36.47963 at 40iterations 1.024972 18.74235 at 50iterations 0.5840476 10.94355 at 60iterations 0.3343571 6.373787 at 70iterations 0.1903205 3.483252 at 80iterations 0.1081681 2.062011 at 90iterations 6.1716057E-02 1.132393 at 100iterations 3.5133794E-02 0.6850586 at 110iterations 2.0004019E-02 0.3669443 at 120iterations 1.1415975E-02 0.2008610 at 130iterations 6.5169022E-03 0.1266174 at 140iterations 3.6980689E-03 6.8042755E-02 at 150iterations 2.1084661E-03 3.8795471E-02 at 160iterations 1.2032974E-03 2.3584366E-02 at 170iterations 6.8502576E-04 1.2475491E-02 at 180iterations finished qdiffx linear iterations at : 17:05:58 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 6.8502576E-04 1.2475491E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 17:05:59 12.570u 0.250s 0:13.21 97.0% 0+0k 0+0io 0pf+0w