Sat Oct 8 11:36:42 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 Sat Oct 8 2011 at 11:36:42 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6323044 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 0.6323044 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -2.699966 assigned positive charge : 508.5883 centred at (gu) : 90.84634 89.61381 91.08894 assigned negative charge : -511.2896 centred at (gu) : 90.62827 89.71352 91.07146 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8632 nv = 96 ne = 84 npr = 70868 no. pairs analyzed = 70868 no. exposed pairs = 3615 no. arc points = 24601 no. surface atoms = 1242 nbur = 2096 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 5235 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3600000 number of dielectric boundary points 3820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2491 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4504609E-09 -1.5659609E-09 midg,1,midg; midg,igrid,midg 9.6084447E-09 -1.4664447E-08 1,midg,midg; igrid,midg,midg -2.5905505E-08 2.7776030E-08 gauss-seidel spectral radius is 0.9870937 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 11:36:43 rms-change max change #iterations 0.1626906 23.91775 at 10iterations 1.5791591E-02 2.015025 at 20iterations 1.5358479E-03 0.1824150 at 30iterations 1.5122302E-04 1.9660950E-02 at 40iterations 1.5147069E-05 1.9035339E-03 at 50iterations finished qdiffx linear iterations at : 11:36:45 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.5147069E-05 1.9035339E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 11:36:46 3.434u 0.208s 0:04.22 86.0% 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 Sat Oct 8 2011 at 11:36:46 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.896913 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 1.896913 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -2.699966 assigned positive charge : 508.5883 centred at (gu) : 92.53816 88.84020 93.26563 assigned negative charge : -511.2896 centred at (gu) : 91.88403 89.14013 93.21387 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 93883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24601 grid for indexing accessible points = 1.400000 m= 36978 mr = 68929 m= 6196 mr = 29082 m= 325 mr = 4216 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1218 time to turn everything in is 0.6700000 number of dielectric boundary points 35057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 25071 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) : 0.6323044 object centre at (A) : 56.77800 53.44000 21.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5012437E-02 -2.7669316E-02 midg,1,midg; midg,igrid,midg 7.5992327E-03 -3.0283252E-02 1,midg,midg; igrid,midg,midg -3.8677085E-02 3.5829902E-02 gauss-seidel spectral radius is 0.9986776 estimated iterations to convergence 218 setup time was (sec) 0.9800000 now iterating at: 11:36:47 rms-change max change #iterations 4.923061 183.7687 at 10iterations 2.333794 74.95114 at 20iterations 1.108698 31.30229 at 30iterations 0.5272250 15.66158 at 40iterations 0.2500162 7.121766 at 50iterations 0.1192886 3.279297 at 60iterations 5.6350660E-02 1.464522 at 70iterations 2.6830679E-02 0.8112020 at 80iterations 1.2745513E-02 0.3716736 at 90iterations 6.0458393E-03 0.1896877 at 100iterations 2.8859933E-03 7.9081774E-02 at 110iterations 1.3716263E-03 3.6899567E-02 at 120iterations finished qdiffx linear iterations at : 11:36:57 total time elapsed so far: 10.84000 # loops : 120 mean,max change (kT/e) : 1.3716263E-03 3.6899567E-02 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 11:36:58 11.019u 0.277s 0:11.76 95.9% 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 Sat Oct 8 2011 at 11:36:58 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3338 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.845370 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): 32.08200 81.47400 ymin,ymax (A): 25.28900 81.59100 zmin,zma (A): -2.982000 46.36000 x,y,z range (A): 49.39200 56.30199 49.34200 scale (grids/A): 2.845370 object centre (A): 56.77800 53.44000 21.68900 number of atom coordinates read : 3338 total number of charged atoms : 3187 net assigned charge : -2.699966 assigned positive charge : 508.5883 centred at (gu) : 93.80705 88.26030 94.89834 assigned negative charge : -511.2896 centred at (gu) : 92.82578 88.71030 94.82075 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 217304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24601 grid for indexing accessible points = 1.400000 m= 117126 mr = 165925 m= 45930 mr = 99489 m= 11428 mr = 38894 m= 1449 mr = 8979 m= 61 mr = 963 m= 0 mr = 13 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 4133 time to turn everything in is 1.730000 number of dielectric boundary points 79035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 25496 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) : 1.896913 object centre at (A) : 56.77800 53.44000 21.68900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1763982 -0.2760603 midg,1,midg; midg,igrid,midg 0.1761387 0.1465373 1,midg,midg; igrid,midg,midg -0.3836898 0.4220761 gauss-seidel spectral radius is 0.9992721 estimated iterations to convergence 292 setup time was (sec) 2.070000 now iterating at: 11:37:00 rms-change max change #iterations 11.41986 337.3458 at 10iterations 6.687267 122.5585 at 20iterations 3.890187 71.27025 at 30iterations 2.260933 38.47702 at 40iterations 1.314596 22.84161 at 50iterations 0.7600720 11.81006 at 60iterations 0.4409821 6.797737 at 70iterations 0.2545594 3.850425 at 80iterations 0.1474399 2.320724 at 90iterations 8.5068718E-02 1.561504 at 100iterations 4.9155403E-02 0.7864418 at 110iterations 2.8387515E-02 0.4453278 at 120iterations 1.6441450E-02 0.2724075 at 130iterations 9.4929300E-03 0.1477966 at 140iterations 5.4807458E-03 8.9272499E-02 at 150iterations 3.1650774E-03 5.1869392E-02 at 160iterations 1.8306512E-03 3.0925751E-02 at 170iterations 1.0588422E-03 1.6792297E-02 at 180iterations finished qdiffx linear iterations at : 11:37:13 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 1.0588422E-03 1.6792297E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 11:37:14 15.517u 0.282s 0:16.18 97.5% 0+0k 0+0io 0pf+0w