Mon Oct 10 14:06:41 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 14:06:42 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5945025 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): 13.18700 65.05800 ymin,ymax (A): 2.108000 56.35500 zmin,zma (A): 86.02100 145.9030 x,y,z range (A): 51.87100 54.24700 59.88200 scale (grids/A): 0.5945025 object centre (A): 39.12250 29.23150 115.9620 number of atom coordinates read : 3048 total number of charged atoms : 2900 net assigned charge : -6.773973 assigned positive charge : 453.4016 centred at (gu) : 90.13033 92.04675 90.13978 assigned negative charge : -460.1769 centred at (gu) : 89.94834 91.92241 90.16686 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7086 nv = 96 ne = 84 npr = 62645 no. pairs analyzed = 62645 no. exposed pairs = 3714 no. arc points = 25991 no. surface atoms = 1247 nbur = 1801 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3910 m= 0 mr = 21 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3500000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2688 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4884705E-09 -3.6115375E-09 midg,1,midg; midg,igrid,midg -4.4611488E-09 3.2291416E-09 1,midg,midg; igrid,midg,midg -8.9863850E-09 4.0782164E-09 gauss-seidel spectral radius is 0.9853939 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 14:06:43 rms-change max change #iterations 0.1123100 19.06947 at 10iterations 1.0077989E-02 1.443872 at 20iterations 1.6583975E-03 0.3228416 at 30iterations 6.8094907E-04 0.1453972 at 40iterations 3.0851792E-04 6.5967560E-02 at 50iterations finished qdiffx linear iterations at : 14:06:47 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 3.0851792E-04 6.5967560E-02 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 14:06:47 4.774u 0.385s 0:05.50 93.6% 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 14:06:47 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.783507 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): 13.18700 65.05800 ymin,ymax (A): 2.108000 56.35500 zmin,zma (A): 86.02100 145.9030 x,y,z range (A): 51.87100 54.24700 59.88200 scale (grids/A): 1.783507 object centre (A): 39.12250 29.23150 115.9620 number of atom coordinates read : 3048 total number of charged atoms : 2900 net assigned charge : -6.773973 assigned positive charge : 453.4016 centred at (gu) : 90.39025 96.13950 90.41869 assigned negative charge : -460.1769 centred at (gu) : 89.84470 95.76666 90.50036 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25991 grid for indexing accessible points = 1.400000 m= 25865 mr = 54536 m= 3229 mr = 18553 m= 128 mr = 1754 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1975 time to turn everything in is 0.6300000 number of dielectric boundary points 32206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22592 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) : 0.5945025 object centre at (A) : 39.12250 29.23150 115.9620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9539278E-02 -1.5059925E-02 midg,1,midg; midg,igrid,midg -3.8477931E-02 -2.5492243E-03 1,midg,midg; igrid,midg,midg -1.8056685E-02 4.5133750E-03 gauss-seidel spectral radius is 0.9984915 estimated iterations to convergence 204 setup time was (sec) 0.9500000 now iterating at: 14:06:48 rms-change max change #iterations 4.073026 156.9830 at 10iterations 1.826086 64.71740 at 20iterations 0.8286390 30.12666 at 30iterations 0.3727975 12.46227 at 40iterations 0.1677808 5.189044 at 50iterations 7.6030552E-02 2.405610 at 60iterations 3.4446236E-02 1.210023 at 70iterations 1.5852878E-02 0.5469494 at 80iterations 7.4615120E-03 0.2672386 at 90iterations 3.8007991E-03 0.1419754 at 100iterations 2.1730680E-03 9.0122223E-02 at 110iterations 1.4195424E-03 5.9345245E-02 at 120iterations finished qdiffx linear iterations at : 14:06:59 total time elapsed so far: 11.10000 # loops : 120 mean,max change (kT/e) : 1.4195424E-03 5.9345245E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 14:06:59 11.293u 0.419s 0:12.03 97.2% 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 Mon Oct 10 2011 at 14:06:59 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.675261 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): 13.18700 65.05800 ymin,ymax (A): 2.108000 56.35500 zmin,zma (A): 86.02100 145.9030 x,y,z range (A): 51.87100 54.24700 59.88200 scale (grids/A): 2.675261 object centre (A): 39.12250 29.23150 115.9620 number of atom coordinates read : 3048 total number of charged atoms : 2900 net assigned charge : -6.773973 assigned positive charge : 453.4016 centred at (gu) : 90.58499 99.20898 90.62768 assigned negative charge : -460.1769 centred at (gu) : 89.76700 98.64999 90.75055 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25991 grid for indexing accessible points = 1.400000 m= 87449 mr = 132769 m= 27473 mr = 70835 m= 5432 mr = 21257 m= 545 mr = 3750 m= 16 mr = 317 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 6464 time to turn everything in is 1.610000 number of dielectric boundary points 72702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 23181 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) : 1.783507 object centre at (A) : 39.12250 29.23150 115.9620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1898416 -0.1991404 midg,1,midg; midg,igrid,midg -0.5782499 -2.4775060E-02 1,midg,midg; igrid,midg,midg -8.5685030E-02 9.1499938E-03 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 1.940000 now iterating at: 14:07:02 rms-change max change #iterations 9.971951 286.6583 at 10iterations 5.785722 148.7250 at 20iterations 3.335381 80.84475 at 30iterations 1.918397 44.27184 at 40iterations 1.099729 23.34332 at 50iterations 0.6285125 12.25564 at 60iterations 0.3598355 7.205500 at 70iterations 0.2054497 4.361526 at 80iterations 0.1171338 2.251915 at 90iterations 6.6790901E-02 1.303638 at 100iterations 3.8165990E-02 0.7080994 at 110iterations 2.1775357E-02 0.4053116 at 120iterations 1.2484612E-02 0.2798080 at 130iterations 7.2319037E-03 0.1676226 at 140iterations 4.2732279E-03 9.0978622E-02 at 150iterations 2.6258789E-03 6.0108185E-02 at 160iterations 1.7177076E-03 4.0002823E-02 at 170iterations 1.2175781E-03 3.2518387E-02 at 180iterations finished qdiffx linear iterations at : 14:07:18 total time elapsed so far: 18.63000 # loops : 180 mean,max change (kT/e) : 1.2175781E-03 3.2518387E-02 energy calculations done at 18.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.79000 DelPhi exited at 14:07:19 18.793u 0.463s 0:19.65 97.9% 0+0k 0+0io 0pf+0w