Mon Oct 10 16:10:16 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+sph.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 = amb.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 16:10:16 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 840 has a net charge of 1.4000 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: 0.5532933 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): 7.630000 62.86400 ymin,ymax (A): -29.63600 34.70600 zmin,zma (A): -29.29000 33.45100 x,y,z range (A): 55.23400 64.34200 62.74100 scale (grids/A): 0.5532933 object centre (A): 35.24700 2.535001 2.080501 number of atom coordinates read : 4603 total number of charged atoms : 4451 net assigned charge : 7.200025 assigned positive charge : 693.4823 centred at (gu) : 89.67812 89.91779 88.70670 assigned negative charge : -686.2863 centred at (gu) : 89.66778 89.88320 88.71515 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9034 nv = 96 ne = 84 npr = 94095 no. pairs analyzed = 94095 no. exposed pairs = 5677 no. arc points = 38502 no. surface atoms = 1916 nbur = 2687 mkacc time = 0.3200000 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 = 1.540000 m= 363 mr = 4933 m= 0 mr = 19 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 4445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3926 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 12028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6404407E-10 3.5488501E-10 midg,1,midg; midg,igrid,midg 1.2882717E-10 1.0341119E-09 1,midg,midg; igrid,midg,midg 4.8947552E-10 6.7726585E-10 gauss-seidel spectral radius is 0.9832733 estimated iterations to convergence 64 setup time was (sec) 0.9200000 now iterating at: 16:10:17 rms-change max change #iterations 9.8498143E-02 14.28643 at 10iterations 7.0823464E-03 0.9841766 at 20iterations 6.7988574E-04 0.1214066 at 30iterations 1.8039743E-04 3.1270981E-02 at 40iterations 7.0449052E-05 9.8648071E-03 at 50iterations finished qdiffx linear iterations at : 16:10:21 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 7.0449052E-05 9.8648071E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 16:10:21 4.728u 0.424s 0:05.42 94.8% 0+0k 0+0io 6pf+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 16:10:21 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 840 has a net charge of 1.4000 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: 1.659880 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): 7.630000 62.86400 ymin,ymax (A): -29.63600 34.70600 zmin,zma (A): -29.29000 33.45100 x,y,z range (A): 55.23400 64.34200 62.74100 scale (grids/A): 1.659880 object centre (A): 35.24700 2.535001 2.080501 number of atom coordinates read : 4603 total number of charged atoms : 4451 net assigned charge : 7.200025 assigned positive charge : 693.4823 centred at (gu) : 89.03309 89.75219 86.11894 assigned negative charge : -686.2863 centred at (gu) : 89.00302 89.64925 86.14503 start vw surface at 0.2200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 101642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38502 grid for indexing accessible points = 1.400000 m= 32946 mr = 71971 m= 3760 mr = 23031 m= 106 mr = 1905 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 426 time to turn everything in is 1.010000 number of dielectric boundary points 41537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 34202 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) : 0.5532933 object centre at (A) : 35.24700 2.535001 2.080501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5663607E-02 7.8449666E-04 midg,1,midg; midg,igrid,midg 2.2242110E-02 8.4133875E-03 1,midg,midg; igrid,midg,midg 5.0209169E-03 4.5314464E-03 gauss-seidel spectral radius is 0.9984077 estimated iterations to convergence 199 setup time was (sec) 1.340000 now iterating at: 16:10:23 rms-change max change #iterations 4.404856 159.7894 at 10iterations 1.939444 57.98997 at 20iterations 0.8560991 26.07663 at 30iterations 0.3778468 10.62535 at 40iterations 0.1666458 5.018538 at 50iterations 7.3473834E-02 2.072984 at 60iterations 3.2512903E-02 0.8847446 at 70iterations 1.4352912E-02 0.4183998 at 80iterations 6.3873227E-03 0.2106888 at 90iterations 2.8739818E-03 8.1166267E-02 at 100iterations 1.3078692E-03 3.8845539E-02 at 110iterations 6.2899751E-04 1.9367218E-02 at 120iterations finished qdiffx linear iterations at : 16:10:33 total time elapsed so far: 10.88000 # loops : 120 mean,max change (kT/e) : 6.2899751E-04 1.9367218E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 16:10:33 11.109u 0.452s 0:11.85 97.4% 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 16:10:33 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 840 has a net charge of 1.4000 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: 2.489820 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): 7.630000 62.86400 ymin,ymax (A): -29.63600 34.70600 zmin,zma (A): -29.29000 33.45100 x,y,z range (A): 55.23400 64.34200 62.74100 scale (grids/A): 2.489820 object centre (A): 35.24700 2.535001 2.080501 number of atom coordinates read : 4603 total number of charged atoms : 4451 net assigned charge : 7.200025 assigned positive charge : 693.4823 centred at (gu) : 88.54923 89.62779 84.17803 assigned negative charge : -686.2863 centred at (gu) : 88.50452 89.47375 84.21748 start vw surface at 0.2300000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 236376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38502 grid for indexing accessible points = 1.400000 m= 113026 mr = 175850 m= 34015 mr = 90256 m= 5945 mr = 25877 m= 454 mr = 3890 m= 4 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 1.590000 no. cavity mid-points inaccessible to solvent = 1370 time to turn everything in is 2.570000 number of dielectric boundary points 93748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.760000 number of grid points assigned charge 35579 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) : 1.659880 object centre at (A) : 35.24700 2.535001 2.080501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4040314 -5.0028358E-02 midg,1,midg; midg,igrid,midg 0.4503404 6.1896190E-02 1,midg,midg; igrid,midg,midg 7.8637160E-02 9.3943805E-02 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 2.980000 now iterating at: 16:10:37 rms-change max change #iterations 11.36514 339.3156 at 10iterations 6.719876 147.3336 at 20iterations 3.938521 85.42107 at 30iterations 2.299128 55.43713 at 40iterations 1.336018 30.11960 at 50iterations 0.7741811 14.00405 at 60iterations 0.4487445 8.024033 at 70iterations 0.2584132 4.607960 at 80iterations 0.1488568 2.949173 at 90iterations 8.5615471E-02 1.534994 at 100iterations 4.9211580E-02 0.8214207 at 110iterations 2.8284397E-02 0.4579582 at 120iterations 1.6252574E-02 0.2822822 at 130iterations 9.3479576E-03 0.1544418 at 140iterations 5.3840978E-03 9.2821121E-02 at 150iterations 3.1143022E-03 5.2351594E-02 at 160iterations 1.8164486E-03 3.2196045E-02 at 170iterations 1.0785939E-03 1.9115448E-02 at 180iterations finished qdiffx linear iterations at : 16:10:57 total time elapsed so far: 22.89000 # loops : 180 mean,max change (kT/e) : 1.0785939E-03 1.9115448E-02 energy calculations done at 22.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.11000 DelPhi exited at 16:10:57 23.110u 0.463s 0:23.88 98.7% 0+0k 0+0io 0pf+0w