Mon Oct 10 09:44:02 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 09:44:02 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5477092 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): -43.08500 21.91300 ymin,ymax (A): 109.8060 166.5430 zmin,zma (A): 155.6280 208.1850 x,y,z range (A): 64.99800 56.73700 52.55701 scale (grids/A): 0.5477092 object centre (A): -10.58600 138.1745 181.9065 number of atom coordinates read : 2841 total number of charged atoms : 2690 net assigned charge : 8.014018 assigned positive charge : 416.1969 centred at (gu) : 88.38570 89.21632 86.99526 assigned negative charge : -408.1833 centred at (gu) : 88.27005 89.19467 86.87424 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5699 nv = 96 ne = 84 npr = 55271 no. pairs analyzed = 55271 no. exposed pairs = 4315 no. arc points = 31036 no. surface atoms = 1415 nbur = 1426 mkacc time = 9.9999994E-02 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 = 1.568000 m= 240 mr = 2475 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3015 ## 391 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7378 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1213744E-10 6.4275979E-10 midg,1,midg; midg,igrid,midg 5.1625809E-10 5.8394689E-10 1,midg,midg; igrid,midg,midg -2.9070121E-10 8.7447904E-10 gauss-seidel spectral radius is 0.9828183 estimated iterations to convergence 63 setup time was (sec) 0.3900000 now iterating at: 09:44:02 rms-change max change #iterations 7.2651945E-02 13.50760 at 10iterations 4.7007021E-03 0.7633667 at 20iterations 3.3119507E-04 5.6462765E-02 at 30iterations 3.1894102E-05 5.0950050E-03 at 40iterations 5.9580375E-06 7.3432922E-04 at 50iterations finished qdiffx linear iterations at : 09:44:05 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.9580375E-06 7.3432922E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 09:44:06 3.429u 0.179s 0:03.93 91.3% 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 09:44:06 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.643127 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): -43.08500 21.91300 ymin,ymax (A): 109.8060 166.5430 zmin,zma (A): 155.6280 208.1850 x,y,z range (A): 64.99800 56.73700 52.55701 scale (grids/A): 1.643127 object centre (A): -10.58600 138.1745 181.9065 number of atom coordinates read : 2841 total number of charged atoms : 2690 net assigned charge : 8.014018 assigned positive charge : 416.1969 centred at (gu) : 85.15632 87.64867 80.98524 assigned negative charge : -408.1833 centred at (gu) : 84.80994 87.58389 80.62237 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31036 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18277 mr = 37535 m= 1920 mr = 11442 m= 65 mr = 771 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 0.3200000 number of dielectric boundary points 32201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20666 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) : 0.5477092 object centre at (A) : -10.58600 138.1745 181.9065 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4476181E-03 5.9195887E-03 midg,1,midg; midg,igrid,midg 5.0616995E-03 2.0256482E-02 1,midg,midg; igrid,midg,midg -1.6276732E-02 1.5662391E-02 gauss-seidel spectral radius is 0.9982076 estimated iterations to convergence 188 setup time was (sec) 0.5300000 now iterating at: 09:44:07 rms-change max change #iterations 3.219746 150.3566 at 10iterations 1.341206 56.48278 at 20iterations 0.5587525 20.71195 at 30iterations 0.2328151 9.391531 at 40iterations 9.7080268E-02 3.641075 at 50iterations 4.0654041E-02 1.583759 at 60iterations 1.7040212E-02 0.6059120 at 70iterations 7.1219453E-03 0.2586632 at 80iterations 2.9738201E-03 0.1114883 at 90iterations 1.2524762E-03 5.3936005E-02 at 100iterations 5.2370946E-04 1.8650055E-02 at 110iterations 2.2070279E-04 7.5073242E-03 at 120iterations finished qdiffx linear iterations at : 09:44:14 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.2070279E-04 7.5073242E-03 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 09:44:14 7.743u 0.202s 0:08.23 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 09:44:14 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.464691 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): -43.08500 21.91300 ymin,ymax (A): 109.8060 166.5430 zmin,zma (A): 155.6280 208.1850 x,y,z range (A): 64.99800 56.73700 52.55701 scale (grids/A): 2.464691 object centre (A): -10.58600 138.1745 181.9065 number of atom coordinates read : 2841 total number of charged atoms : 2690 net assigned charge : 8.014018 assigned positive charge : 416.1969 centred at (gu) : 82.73431 86.47281 76.47757 assigned negative charge : -408.1833 centred at (gu) : 82.21495 86.37567 75.93349 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 142726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31036 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62216 mr = 92976 m= 17893 mr = 46140 m= 2805 mr = 12523 m= 165 mr = 1491 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 625 time to turn everything in is 0.7700000 number of dielectric boundary points 72621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21499 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) : 1.643127 object centre at (A) : -10.58600 138.1745 181.9065 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1329428E-02 7.0084743E-02 midg,1,midg; midg,igrid,midg 1.0591715E-02 0.4148313 1,midg,midg; igrid,midg,midg -0.6171274 0.6323212 gauss-seidel spectral radius is 0.9991500 estimated iterations to convergence 271 setup time was (sec) 1.010000 now iterating at: 09:44:15 rms-change max change #iterations 8.585309 266.8170 at 10iterations 4.926550 167.2815 at 20iterations 2.793749 76.59347 at 30iterations 1.572871 37.25877 at 40iterations 0.8827304 23.99953 at 50iterations 0.4934636 12.30548 at 60iterations 0.2750050 7.809898 at 70iterations 0.1530643 4.217072 at 80iterations 8.4903739E-02 2.381008 at 90iterations 4.7093749E-02 1.240804 at 100iterations 2.6044581E-02 0.7168045 at 110iterations 1.4439818E-02 0.3572752 at 120iterations 7.9739783E-03 0.1738091 at 130iterations 4.4088196E-03 0.1038589 at 140iterations 2.4390295E-03 5.3997040E-02 at 150iterations 1.3462355E-03 3.5343289E-02 at 160iterations 7.4450969E-04 1.6250610E-02 at 170iterations 4.1041500E-04 8.5487366E-03 at 180iterations finished qdiffx linear iterations at : 09:44:27 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 4.1041500E-04 8.5487366E-03 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 09:44:27 12.361u 0.184s 0:12.82 97.8% 0+0k 0+0io 0pf+0w