Sun Oct 9 14:44:18 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 14:44:18 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: ADP 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5641838 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): -27.04000 26.64200 ymin,ymax (A): -26.23800 36.86200 zmin,zma (A): -19.97400 40.27700 x,y,z range (A): 53.68200 63.10000 60.25100 scale (grids/A): 0.5641838 object centre (A): -0.1989994 5.312002 10.15150 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 3.500015 assigned positive charge : 456.6220 centred at (gu) : 89.98061 89.91757 88.79182 assigned negative charge : -453.1233 centred at (gu) : 89.95574 90.11558 88.90885 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6410 nv = 96 ne = 84 npr = 57958 no. pairs analyzed = 57958 no. exposed pairs = 4041 no. arc points = 29776 no. surface atoms = 1340 nbur = 1659 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 = 1.512000 m= 285 mr = 3020 m= 1 mr = 11 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 0.2300000 number of dielectric boundary points 3665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3026 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8174 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5822975E-09 -8.4428453E-10 midg,1,midg; midg,igrid,midg 3.0030118E-09 -2.1943902E-09 1,midg,midg; igrid,midg,midg 8.8652752E-11 7.3573586E-10 gauss-seidel spectral radius is 0.9838095 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 14:44:19 rms-change max change #iterations 8.3824277E-02 14.36713 at 10iterations 6.2001888E-03 0.9706230 at 20iterations 4.4661257E-04 7.2690964E-02 at 30iterations 3.3443768E-05 5.3482056E-03 at 40iterations 2.7242136E-06 4.5013428E-04 at 50iterations finished qdiffx linear iterations at : 14:44:21 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.7242136E-06 4.5013428E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:44:22 3.454u 0.162s 0:03.88 93.0% 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 Sun Oct 9 2011 at 14:44:22 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: ADP 522 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.692551 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): -27.04000 26.64200 ymin,ymax (A): -26.23800 36.86200 zmin,zma (A): -19.97400 40.27700 x,y,z range (A): 53.68200 63.10000 60.25100 scale (grids/A): 1.692551 object centre (A): -0.1989994 5.312002 10.15150 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 3.500015 assigned positive charge : 456.6220 centred at (gu) : 89.94105 89.75220 86.37446 assigned negative charge : -453.1233 centred at (gu) : 89.86700 90.34642 86.72636 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70068 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29776 grid for indexing accessible points = 1.400000 m= 20225 mr = 44810 m= 2212 mr = 12943 m= 76 mr = 982 m= 0 mr = 13 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 301 time to turn everything in is 0.3600000 number of dielectric boundary points 33833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22053 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) : 0.5641838 object centre at (A) : -0.1989994 5.312002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2983046E-02 -6.0686213E-03 midg,1,midg; midg,igrid,midg 1.9178031E-02 -1.4931682E-02 1,midg,midg; igrid,midg,midg 1.1645613E-03 -1.3577468E-02 gauss-seidel spectral radius is 0.9983334 estimated iterations to convergence 194 setup time was (sec) 0.5800000 now iterating at: 14:44:23 rms-change max change #iterations 3.654629 154.8834 at 10iterations 1.571385 62.26192 at 20iterations 0.6789013 25.84360 at 30iterations 0.2917930 10.74048 at 40iterations 0.1259335 4.542666 at 50iterations 5.4326672E-02 2.033737 at 60iterations 2.3360237E-02 0.8144226 at 70iterations 1.0121274E-02 0.3291397 at 80iterations 4.3512308E-03 0.1412201 at 90iterations 1.8785637E-03 6.9133759E-02 at 100iterations 8.1231940E-04 2.7988434E-02 at 110iterations 3.5037717E-04 1.1394501E-02 at 120iterations finished qdiffx linear iterations at : 14:44:30 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.5037717E-04 1.1394501E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:44:30 7.843u 0.202s 0:08.35 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 Sun Oct 9 2011 at 14:44:30 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: ADP 522 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.538827 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): -27.04000 26.64200 ymin,ymax (A): -26.23800 36.86200 zmin,zma (A): -19.97400 40.27700 x,y,z range (A): 53.68200 63.10000 60.25100 scale (grids/A): 2.538827 object centre (A): -0.1989994 5.312002 10.15150 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 3.500015 assigned positive charge : 456.6220 centred at (gu) : 89.91135 89.62799 84.56149 assigned negative charge : -453.1233 centred at (gu) : 89.80038 90.51955 85.08936 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29776 grid for indexing accessible points = 1.400000 m= 70485 mr = 110115 m= 19492 mr = 53740 m= 3280 mr = 13555 m= 281 mr = 1993 m= 9 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 0.8300000 number of dielectric boundary points 76438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22834 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) : 1.692551 object centre at (A) : -0.1989994 5.312002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5615035 -0.1361898 midg,1,midg; midg,igrid,midg 0.1757211 -0.1545585 1,midg,midg; igrid,midg,midg 5.2134629E-02 -0.2363272 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.070000 now iterating at: 14:44:32 rms-change max change #iterations 9.448674 380.6465 at 10iterations 5.433008 151.3315 at 20iterations 3.103495 76.23668 at 30iterations 1.763603 42.89540 at 40iterations 1.001912 22.90498 at 50iterations 0.5667667 12.79968 at 60iterations 0.3200446 8.195120 at 70iterations 0.1802027 3.914486 at 80iterations 0.1016355 2.305837 at 90iterations 5.7050001E-02 1.239075 at 100iterations 3.2128260E-02 0.6580682 at 110iterations 1.8028561E-02 0.4038296 at 120iterations 1.0098998E-02 0.1915070 at 130iterations 5.6814519E-03 0.1317482 at 140iterations 3.1838000E-03 6.6966057E-02 at 150iterations 1.7853320E-03 3.6251068E-02 at 160iterations 1.0022559E-03 2.0639658E-02 at 170iterations 5.6387100E-04 1.1784554E-02 at 180iterations finished qdiffx linear iterations at : 14:44:43 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 5.6387100E-04 1.1784554E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 14:44:44 12.674u 0.213s 0:13.18 97.7% 0+0k 0+0io 0pf+0w