Sun Oct 9 22:32:08 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 Sun Oct 9 2011 at 22:32:08 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 0.6213240 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): 3.520000 54.61800 ymin,ymax (A): 17.47200 74.76900 zmin,zma (A): 59.23200 112.9300 x,y,z range (A): 51.09800 57.29700 53.69800 scale (grids/A): 0.6213240 object centre (A): 29.06900 46.12050 86.08100 number of atom coordinates read : 3026 total number of charged atoms : 2929 net assigned charge : 4.525016 assigned positive charge : 468.6359 centred at (gu) : 89.18676 90.49616 89.54876 assigned negative charge : -464.1120 centred at (gu) : 89.20856 90.48138 89.66376 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8037 nv = 96 ne = 84 npr = 56314 no. pairs analyzed = 56314 no. exposed pairs = 4240 no. arc points = 30730 no. surface atoms = 1404 nbur = 1622 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 3974 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3500000 number of dielectric boundary points 4467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3050 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4473755E-08 -5.3102136E-09 midg,1,midg; midg,igrid,midg 2.2592754E-09 5.5009362E-09 1,midg,midg; igrid,midg,midg 6.5854646E-09 1.6319037E-09 gauss-seidel spectral radius is 0.9866410 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 22:32:09 rms-change max change #iterations 0.1349076 21.09231 at 10iterations 1.2697541E-02 1.840460 at 20iterations 1.1638980E-03 0.1903391 at 30iterations 1.1049090E-04 1.6235352E-02 at 40iterations 1.1816305E-05 1.5144348E-03 at 50iterations finished qdiffx linear iterations at : 22:32:12 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1816305E-05 1.5144348E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 22:32:12 3.413u 0.123s 0:03.82 92.4% 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 Sun Oct 9 2011 at 22:32:12 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 1.863972 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): 3.520000 54.61800 ymin,ymax (A): 17.47200 74.76900 zmin,zma (A): 59.23200 112.9300 x,y,z range (A): 51.09800 57.29700 53.69800 scale (grids/A): 1.863972 object centre (A): 29.06900 46.12050 86.08100 number of atom coordinates read : 3026 total number of charged atoms : 2929 net assigned charge : 4.525016 assigned positive charge : 468.6359 centred at (gu) : 87.55922 91.48792 88.64584 assigned negative charge : -464.1120 centred at (gu) : 87.62547 91.44357 88.99068 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30730 grid for indexing accessible points = 1.400000 m= 29302 mr = 55601 m= 4383 mr = 20361 m= 258 mr = 2487 m= 1 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 287 time to turn everything in is 0.6200000 number of dielectric boundary points 41373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22955 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) : 0.6213240 object centre at (A) : 29.06900 46.12050 86.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2198548E-02 -1.1452770E-02 midg,1,midg; midg,igrid,midg 3.0038770E-02 -1.4045257E-02 1,midg,midg; igrid,midg,midg 1.7682211E-02 1.5924321E-02 gauss-seidel spectral radius is 0.9986557 estimated iterations to convergence 216 setup time was (sec) 0.9000000 now iterating at: 22:32:13 rms-change max change #iterations 4.515760 181.3429 at 10iterations 2.114340 70.21811 at 20iterations 0.9917212 31.29133 at 30iterations 0.4636129 13.66935 at 40iterations 0.2175778 7.143870 at 50iterations 0.1023517 3.210837 at 60iterations 4.8045047E-02 1.534499 at 70iterations 2.2577763E-02 0.6720772 at 80iterations 1.0610829E-02 0.3127441 at 90iterations 5.0009163E-03 0.1485443 at 100iterations 2.3526466E-03 8.6559296E-02 at 110iterations 1.1075797E-03 3.4420967E-02 at 120iterations finished qdiffx linear iterations at : 22:32:20 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.1075797E-03 3.4420967E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 22:32:21 7.695u 0.174s 0:08.22 95.6% 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 Sun Oct 9 2011 at 22:32:21 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 2.795958 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): 3.520000 54.61800 ymin,ymax (A): 17.47200 74.76900 zmin,zma (A): 59.23200 112.9300 x,y,z range (A): 51.09800 57.29700 53.69800 scale (grids/A): 2.795958 object centre (A): 29.06900 46.12050 86.08100 number of atom coordinates read : 3026 total number of charged atoms : 2929 net assigned charge : 4.525016 assigned positive charge : 468.6359 centred at (gu) : 86.33870 92.23164 87.96851 assigned negative charge : -464.1120 centred at (gu) : 86.43805 92.16520 88.48605 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 198282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30730 grid for indexing accessible points = 1.400000 m= 95588 mr = 135677 m= 32951 mr = 75239 m= 7586 mr = 25158 m= 1023 mr = 5323 m= 70 mr = 712 m= 0 mr = 18 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 1.550000 number of dielectric boundary points 93373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 23427 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) : 1.863972 object centre at (A) : 29.06900 46.12050 86.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2910068 -0.1339500 midg,1,midg; midg,igrid,midg 0.3397722 -0.2837629 1,midg,midg; igrid,midg,midg 0.1576828 0.2518839 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 1.860000 now iterating at: 22:32:23 rms-change max change #iterations 10.92090 310.5901 at 10iterations 6.647718 158.9328 at 20iterations 3.992048 103.3201 at 30iterations 2.385351 51.01424 at 40iterations 1.421249 31.72550 at 50iterations 0.8419976 15.88690 at 60iterations 0.4987559 9.318044 at 70iterations 0.2940592 5.113935 at 80iterations 0.1730581 3.247738 at 90iterations 0.1019337 1.893420 at 100iterations 5.9830513E-02 1.058885 at 110iterations 3.5124749E-02 0.6336975 at 120iterations 2.0623926E-02 0.3532934 at 130iterations 1.2118183E-02 0.2198811 at 140iterations 7.0972680E-03 0.1499748 at 150iterations 4.1474877E-03 7.7236176E-02 at 160iterations 2.4276162E-03 4.5776367E-02 at 170iterations 1.4212237E-03 2.4578094E-02 at 180iterations finished qdiffx linear iterations at : 22:32:33 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 1.4212237E-03 2.4578094E-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) 12.64000 DelPhi exited at 22:32:34 12.643u 0.174s 0:13.08 97.9% 0+0k 0+0io 0pf+0w