Mon Oct 10 19:32:53 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 19:32:53 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5643090 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 0.5643090 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2597 net assigned charge : 0.9060291 assigned positive charge : 406.0568 centred at (gu) : 91.12096 90.33714 90.17400 assigned negative charge : -405.1515 centred at (gu) : 91.11715 90.24529 90.16433 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5638 nv = 96 ne = 84 npr = 55710 no. pairs analyzed = 55710 no. exposed pairs = 3397 no. arc points = 24576 no. surface atoms = 1151 nbur = 1590 mkacc time = 0.1500000 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= 241 mr = 2934 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3400000 number of dielectric boundary points 2933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2529 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7346 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7426126E-12 2.3131159E-10 midg,1,midg; midg,igrid,midg -9.0463814E-10 1.2760872E-09 1,midg,midg; igrid,midg,midg 4.9619666E-11 2.0001022E-10 gauss-seidel spectral radius is 0.9837812 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 19:32:54 rms-change max change #iterations 8.1157729E-02 14.71887 at 10iterations 6.0419240E-03 0.9786654 at 20iterations 4.7530598E-04 8.1667423E-02 at 30iterations 5.5363009E-05 1.2855530E-02 at 40iterations 1.0910641E-05 2.8591156E-03 at 50iterations finished qdiffx linear iterations at : 19:32:57 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 1.0910641E-05 2.8591156E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 19:32:58 4.163u 0.278s 0:05.07 87.3% 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 19:32:58 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: GLM 103 has a net charge of -0.0940 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: 1.692927 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 1.692927 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2597 net assigned charge : 0.9060291 assigned positive charge : 406.0568 centred at (gu) : 93.36253 91.01096 90.52179 assigned negative charge : -405.1515 centred at (gu) : 93.35117 90.73578 90.49277 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24576 grid for indexing accessible points = 1.400000 m= 19068 mr = 41604 m= 2132 mr = 13426 m= 46 mr = 1107 m= 0 mr = 7 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2737 time to turn everything in is 0.5500000 number of dielectric boundary points 27063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20043 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) : 0.5643090 object centre at (A) : -8.938500 7.998500 42.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3700568E-02 4.2640148E-03 midg,1,midg; midg,igrid,midg -2.4266690E-03 5.7352902E-03 1,midg,midg; igrid,midg,midg 4.1554151E-03 -2.0112337E-03 gauss-seidel spectral radius is 0.9982914 estimated iterations to convergence 192 setup time was (sec) 0.8600000 now iterating at: 19:32:59 rms-change max change #iterations 3.414350 151.0639 at 10iterations 1.455114 57.14766 at 20iterations 0.6205150 24.35255 at 30iterations 0.2663294 8.638885 at 40iterations 0.1140113 4.314601 at 50iterations 4.8737627E-02 1.850350 at 60iterations 2.0776611E-02 0.7450495 at 70iterations 8.9120427E-03 0.3100033 at 80iterations 3.8267700E-03 0.1390910 at 90iterations 1.6402235E-03 5.5854797E-02 at 100iterations 7.0917053E-04 2.5742531E-02 at 110iterations 3.0753078E-04 1.1714935E-02 at 120iterations finished qdiffx linear iterations at : 19:33:08 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 3.0753078E-04 1.1714935E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 19:33:09 9.434u 0.309s 0:11.29 86.1% 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 19:33:10 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.539390 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 2.539390 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2597 net assigned charge : 0.9060291 assigned positive charge : 406.0568 centred at (gu) : 95.04359 91.51624 90.78255 assigned negative charge : -405.1515 centred at (gu) : 95.02676 91.10357 90.73901 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 143957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24576 grid for indexing accessible points = 1.400000 m= 65494 mr = 102113 m= 19444 mr = 52040 m= 3372 mr = 14878 m= 281 mr = 2340 m= 5 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 9024 time to turn everything in is 1.350000 number of dielectric boundary points 61037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 20766 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) : 1.692927 object centre at (A) : -8.938500 7.998500 42.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2422046 4.0754076E-02 midg,1,midg; midg,igrid,midg -3.1220663E-02 4.9373791E-02 1,midg,midg; igrid,midg,midg 4.4525690E-02 0.1186536 gauss-seidel spectral radius is 0.9991663 estimated iterations to convergence 274 setup time was (sec) 1.670000 now iterating at: 19:33:12 rms-change max change #iterations 8.581697 293.7876 at 10iterations 4.844874 121.6310 at 20iterations 2.714376 62.28381 at 30iterations 1.513587 32.93813 at 40iterations 0.8445324 18.44393 at 50iterations 0.4708953 10.17508 at 60iterations 0.2621798 6.081963 at 70iterations 0.1456033 3.246574 at 80iterations 8.0886908E-02 1.678653 at 90iterations 4.4996984E-02 1.063538 at 100iterations 2.4951415E-02 0.5442810 at 110iterations 1.3833676E-02 0.3084745 at 120iterations 7.7045402E-03 0.1688051 at 130iterations 4.2632064E-03 9.3509197E-02 at 140iterations 2.3760637E-03 5.1226139E-02 at 150iterations 1.3255110E-03 2.8594017E-02 at 160iterations 7.4136886E-04 1.5899658E-02 at 170iterations 4.1808566E-04 9.4091296E-03 at 180iterations finished qdiffx linear iterations at : 19:33:25 total time elapsed so far: 15.40000 # loops : 180 mean,max change (kT/e) : 4.1808566E-04 9.4091296E-03 energy calculations done at 15.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.58000 DelPhi exited at 19:33:26 15.584u 0.318s 0:16.30 97.4% 0+0k 0+0io 0pf+0w