Sun Oct 9 02:52:32 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 02:52:32 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4609 !!! WARNING: SEP 530 has a net charge of -0.4750 !!! WARNING: ASP 584 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5184894 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): 215.1460 276.2470 ymin,ymax (A): 71.72900 140.3900 zmin,zma (A): -69.94200 -6.114000 x,y,z range (A): 61.10098 68.66100 63.82800 scale (grids/A): 0.5184894 object centre (A): 245.6965 106.0595 -38.02800 number of atom coordinates read : 4609 total number of charged atoms : 4472 net assigned charge : 16.02498 assigned positive charge : 689.4416 centred at (gu) : 91.22308 87.32150 90.76775 assigned negative charge : -673.4219 centred at (gu) : 91.29705 87.31412 90.82005 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7800 nv = 96 ne = 84 npr = 91785 no. pairs analyzed = 91785 no. exposed pairs = 6063 no. arc points = 40928 no. surface atoms = 2068 nbur = 2541 mkacc time = 0.2200000 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 = 1.624000 m= 291 mr = 3885 m= 0 mr = 6 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4033 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0969769E-10 1.7585333E-10 midg,1,midg; midg,igrid,midg 5.9206390E-10 1.7868373E-10 1,midg,midg; igrid,midg,midg 4.1717343E-10 9.3464174E-11 gauss-seidel spectral radius is 0.9809651 estimated iterations to convergence 60 setup time was (sec) 0.7300000 now iterating at: 02:52:33 rms-change max change #iterations 6.9243155E-02 10.46292 at 10iterations 5.9391758E-03 0.9711304 at 20iterations 1.5386844E-03 0.2431641 at 30iterations 5.3211791E-04 8.0493927E-02 at 40iterations 1.8698451E-04 2.7336121E-02 at 50iterations finished qdiffx linear iterations at : 02:52:36 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 1.8698451E-04 2.7336121E-02 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 02:52:36 3.755u 0.204s 0:04.28 92.2% 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 02:52:36 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4609 !!! WARNING: SEP 530 has a net charge of -0.4750 !!! WARNING: ASP 584 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.555468 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): 215.1460 276.2470 ymin,ymax (A): 71.72900 140.3900 zmin,zma (A): -69.94200 -6.114000 x,y,z range (A): 61.10098 68.66100 63.82800 scale (grids/A): 1.555468 object centre (A): 245.6965 106.0595 -38.02800 number of atom coordinates read : 4609 total number of charged atoms : 4472 net assigned charge : 16.02498 assigned positive charge : 689.4416 centred at (gu) : 93.66752 81.96281 92.30134 assigned negative charge : -673.4219 centred at (gu) : 93.89073 81.94232 92.45984 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 86627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40928 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26624 mr = 57848 m= 2574 mr = 17824 m= 38 mr = 1116 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.6800000 number of dielectric boundary points 39075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 484 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 33724 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) : 0.5184894 object centre at (A) : 245.6965 106.0595 -38.02800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2792304E-02 5.4398822E-03 midg,1,midg; midg,igrid,midg 3.4390785E-02 1.1469614E-02 1,midg,midg; igrid,midg,midg 8.6410223E-03 3.4170020E-03 gauss-seidel spectral radius is 0.9981619 estimated iterations to convergence 185 setup time was (sec) 1.000000 now iterating at: 02:52:37 rms-change max change #iterations 3.807808 171.1880 at 10iterations 1.573395 59.09662 at 20iterations 0.6498336 25.74663 at 30iterations 0.2696757 8.195470 at 40iterations 0.1120464 3.569317 at 50iterations 4.6961356E-02 1.523911 at 60iterations 1.9799381E-02 0.6640167 at 70iterations 8.5711470E-03 0.3004875 at 80iterations 3.9799088E-03 0.1335678 at 90iterations 2.0350453E-03 7.5576782E-02 at 100iterations 1.1744560E-03 3.8333893E-02 at 110iterations 7.4126036E-04 2.2445679E-02 at 120iterations finished qdiffx linear iterations at : 02:52:45 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 7.4126036E-04 2.2445679E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 02:52:45 8.451u 0.218s 0:08.99 96.3% 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 Sun Oct 9 2011 at 02:52:45 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4609 !!! WARNING: SEP 530 has a net charge of -0.4750 !!! WARNING: ASP 584 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.333202 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): 215.1460 276.2470 ymin,ymax (A): 71.72900 140.3900 zmin,zma (A): -69.94200 -6.114000 x,y,z range (A): 61.10098 68.66100 63.82800 scale (grids/A): 2.333202 object centre (A): 245.6965 106.0595 -38.02800 number of atom coordinates read : 4609 total number of charged atoms : 4472 net assigned charge : 16.02498 assigned positive charge : 689.4416 centred at (gu) : 95.50084 77.94374 93.45156 assigned negative charge : -673.4219 centred at (gu) : 95.83601 77.91332 93.68966 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 201397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40928 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 91783 mr = 142174 m= 26041 mr = 71190 m= 3833 mr = 19237 m= 209 mr = 2341 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 471 time to turn everything in is 1.640000 number of dielectric boundary points 88260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 35689 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) : 1.555468 object centre at (A) : 245.6965 106.0595 -38.02800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5339723 6.4810708E-02 midg,1,midg; midg,igrid,midg 0.5250229 0.1619290 1,midg,midg; igrid,midg,midg 0.1777289 2.1633074E-02 gauss-seidel spectral radius is 0.9991754 estimated iterations to convergence 275 setup time was (sec) 1.990000 now iterating at: 02:52:48 rms-change max change #iterations 10.33619 319.1467 at 10iterations 5.990955 152.1819 at 20iterations 3.435841 83.34440 at 30iterations 1.960130 46.33203 at 40iterations 1.110205 26.20357 at 50iterations 0.6275768 12.11216 at 60iterations 0.3533037 7.275525 at 70iterations 0.1988084 3.769700 at 80iterations 0.1115559 2.274042 at 90iterations 6.2565714E-02 1.241714 at 100iterations 3.5071634E-02 0.6537099 at 110iterations 1.9702870E-02 0.3942690 at 120iterations 1.1082891E-02 0.2158966 at 130iterations 6.2681800E-03 0.1168432 at 140iterations 3.5696004E-03 6.6421509E-02 at 150iterations 2.0760205E-03 3.9218903E-02 at 160iterations 1.2414663E-03 2.7462006E-02 at 170iterations 7.7617599E-04 1.4747620E-02 at 180iterations finished qdiffx linear iterations at : 02:53:01 total time elapsed so far: 14.98000 # loops : 180 mean,max change (kT/e) : 7.7617599E-04 1.4747620E-02 energy calculations done at 14.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.17000 DelPhi exited at 02:53:01 15.173u 0.225s 0:15.68 98.1% 0+0k 0+0io 0pf+0w