Sat Oct 15 15:12:40 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 Sat Oct 15 2011 at 15:12:40 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 69 has a net charge of 0.5140 !!! WARNING: SEP 223 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6678172 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): -12.06500 37.46200 ymin,ymax (A): -26.57300 21.47200 zmin,zma (A): -7.925000 45.38300 x,y,z range (A): 49.52700 48.04500 53.30800 scale (grids/A): 0.6678172 object centre (A): 12.69850 -2.550500 18.72900 number of atom coordinates read : 2734 total number of charged atoms : 2585 net assigned charge : 7.039016 assigned positive charge : 416.1540 centred at (gu) : 90.39449 90.35556 91.21141 assigned negative charge : -409.1154 centred at (gu) : 90.15118 90.18467 91.31358 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8034 nv = 96 ne = 84 npr = 56592 no. pairs analyzed = 56592 no. exposed pairs = 3219 no. arc points = 22220 no. surface atoms = 1092 nbur = 1642 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 4599 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.2100000 number of dielectric boundary points 3816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2265 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7317090E-08 -5.7830225E-09 midg,1,midg; midg,igrid,midg -2.0426674E-08 6.9609321E-08 1,midg,midg; igrid,midg,midg -3.7927041E-08 8.9297025E-08 gauss-seidel spectral radius is 0.9883823 estimated iterations to convergence 76 setup time was (sec) 0.4400000 now iterating at: 15:12:41 rms-change max change #iterations 0.1835461 23.20645 at 10iterations 2.0659661E-02 2.980276 at 20iterations 2.3965382E-03 0.2911758 at 30iterations 3.7147725E-04 4.2160034E-02 at 40iterations 8.8219938E-05 9.3684196E-03 at 50iterations finished qdiffx linear iterations at : 15:12:44 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.8219938E-05 9.3684196E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:12:44 3.556u 0.230s 0:04.18 90.4% 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 Sat Oct 15 2011 at 15:12:44 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 69 has a net charge of 0.5140 !!! WARNING: SEP 223 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.003452 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): -12.06500 37.46200 ymin,ymax (A): -26.57300 21.47200 zmin,zma (A): -7.925000 45.38300 x,y,z range (A): 49.52700 48.04500 53.30800 scale (grids/A): 2.003452 object centre (A): 12.69850 -2.550500 18.72900 number of atom coordinates read : 2734 total number of charged atoms : 2585 net assigned charge : 7.039016 assigned positive charge : 416.1540 centred at (gu) : 91.18291 91.06602 93.63348 assigned negative charge : -409.1154 centred at (gu) : 90.45316 90.55387 93.94047 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22220 grid for indexing accessible points = 1.400000 m= 33091 mr = 61455 m= 5661 mr = 25409 m= 380 mr = 3752 m= 5 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2540 time to turn everything in is 0.4100000 number of dielectric boundary points 34829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20473 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) : 0.6678172 object centre at (A) : 12.69850 -2.550500 18.72900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2021602E-02 -4.2044648E-04 midg,1,midg; midg,igrid,midg -1.6706374E-02 4.0794376E-02 1,midg,midg; igrid,midg,midg -4.7388007E-03 8.8886127E-02 gauss-seidel spectral radius is 0.9987683 estimated iterations to convergence 226 setup time was (sec) 0.6400000 now iterating at: 15:12:45 rms-change max change #iterations 4.879424 241.3229 at 10iterations 2.382089 79.57205 at 20iterations 1.163553 35.07914 at 30iterations 0.5681734 17.65539 at 40iterations 0.2771585 8.536926 at 50iterations 0.1350566 3.920235 at 60iterations 6.6076018E-02 2.045738 at 70iterations 3.2365572E-02 0.9721019 at 80iterations 1.5912687E-02 0.4384012 at 90iterations 7.8445179E-03 0.2158623 at 100iterations 3.9395313E-03 0.1263084 at 110iterations 2.0163634E-03 5.7128906E-02 at 120iterations finished qdiffx linear iterations at : 15:12:52 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.0163634E-03 5.7128906E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 15:12:53 7.897u 0.216s 0:08.78 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 Sat Oct 15 2011 at 15:12:53 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIR 69 has a net charge of 0.5140 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 3.005177 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): -12.06500 37.46200 ymin,ymax (A): -26.57300 21.47200 zmin,zma (A): -7.925000 45.38300 x,y,z range (A): 49.52700 48.04500 53.30800 scale (grids/A): 3.005177 object centre (A): 12.69850 -2.550500 18.72900 number of atom coordinates read : 2734 total number of charged atoms : 2585 net assigned charge : 7.039016 assigned positive charge : 416.1540 centred at (gu) : 91.77430 91.59879 95.45021 assigned negative charge : -409.1154 centred at (gu) : 90.67962 90.83072 95.91058 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 199461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22220 grid for indexing accessible points = 1.400000 m= 105639 mr = 148142 m= 40781 mr = 88272 m= 10372 mr = 33865 m= 1599 mr = 8081 m= 103 mr = 1074 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 8297 time to turn everything in is 1.150000 number of dielectric boundary points 78483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20675 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) : 2.003452 object centre at (A) : 12.69850 -2.550500 18.72900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4447991 0.2138861 midg,1,midg; midg,igrid,midg -0.1929912 0.4409561 1,midg,midg; igrid,midg,midg -2.8255163E-02 0.7426389 gauss-seidel spectral radius is 0.9992876 estimated iterations to convergence 296 setup time was (sec) 1.410000 now iterating at: 15:12:55 rms-change max change #iterations 11.09510 410.8801 at 10iterations 6.532766 166.6717 at 20iterations 3.845549 84.43487 at 30iterations 2.255862 47.38052 at 40iterations 1.323199 27.94108 at 50iterations 0.7754855 14.03562 at 60iterations 0.4524015 9.608154 at 70iterations 0.2644064 4.748445 at 80iterations 0.1545870 3.216595 at 90iterations 9.0223730E-02 1.528862 at 100iterations 5.2542701E-02 0.8450584 at 110iterations 3.0675013E-02 0.6214827 at 120iterations 1.7920969E-02 0.3059397 at 130iterations 1.0530400E-02 0.1870003 at 140iterations 6.1971294E-03 0.1266632 at 150iterations 3.7031330E-03 6.9155693E-02 at 160iterations 2.2521263E-03 3.9184570E-02 at 170iterations 1.4125962E-03 2.7397156E-02 at 180iterations finished qdiffx linear iterations at : 15:13:07 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.4125962E-03 2.7397156E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 15:13:07 13.502u 0.269s 0:14.14 97.3% 0+0k 0+0io 0pf+0w