Mon Oct 10 16:06:16 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+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 Mon Oct 10 2011 at 16:06:16 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4259 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5505892 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): 7.674000 59.37000 ymin,ymax (A): -34.39500 29.57600 zmin,zma (A): -35.37900 29.27900 x,y,z range (A): 51.69600 63.97100 64.65800 scale (grids/A): 0.5505892 object centre (A): 33.52200 -2.409500 -3.050001 number of atom coordinates read : 4259 total number of charged atoms : 4108 net assigned charge : 7.500047 assigned positive charge : 635.7106 centred at (gu) : 89.64769 90.26954 91.27658 assigned negative charge : -628.2137 centred at (gu) : 89.55222 90.27422 91.29584 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8416 nv = 96 ne = 84 npr = 86325 no. pairs analyzed = 86325 no. exposed pairs = 5221 no. arc points = 35793 no. surface atoms = 1747 nbur = 2512 mkacc time = 0.1400000 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 = 1.568000 m= 360 mr = 4603 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 4155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3684 ## 458 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 11079 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7371596E-10 4.7207410E-10 midg,1,midg; midg,igrid,midg 5.7893063E-10 5.4721794E-10 1,midg,midg; igrid,midg,midg -5.5881583E-10 1.4810164E-09 gauss-seidel spectral radius is 0.9830856 estimated iterations to convergence 63 setup time was (sec) 0.4700000 now iterating at: 16:06:16 rms-change max change #iterations 9.3829930E-02 11.82823 at 10iterations 6.7294035E-03 0.9828815 at 20iterations 9.2578196E-04 0.1638260 at 30iterations 3.1092644E-04 4.8927307E-02 at 40iterations 1.2535245E-04 1.6895294E-02 at 50iterations finished qdiffx linear iterations at : 16:06:19 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.2535245E-04 1.6895294E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:06:20 3.462u 0.171s 0:03.90 93.0% 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 Mon Oct 10 2011 at 16:06:20 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4259 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.651768 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): 7.674000 59.37000 ymin,ymax (A): -34.39500 29.57600 zmin,zma (A): -35.37900 29.27900 x,y,z range (A): 51.69600 63.97100 64.65800 scale (grids/A): 1.651768 object centre (A): 33.52200 -2.409500 -3.050001 number of atom coordinates read : 4259 total number of charged atoms : 4108 net assigned charge : 7.500047 assigned positive charge : 635.7106 centred at (gu) : 88.94173 90.80708 93.82851 assigned negative charge : -628.2137 centred at (gu) : 88.65633 90.82198 93.88711 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 94387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35793 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30937 mr = 66996 m= 3374 mr = 21620 m= 99 mr = 1695 m= 0 mr = 8 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.4500000 number of dielectric boundary points 38478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 377 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 31607 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) : 0.5505892 object centre at (A) : 33.52200 -2.409500 -3.050001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1288532E-03 2.4656726E-02 midg,1,midg; midg,igrid,midg 1.7874030E-02 2.0395376E-02 1,midg,midg; igrid,midg,midg 9.2938426E-04 1.2419856E-02 gauss-seidel spectral radius is 0.9983596 estimated iterations to convergence 196 setup time was (sec) 0.6800000 now iterating at: 16:06:20 rms-change max change #iterations 4.152265 157.1833 at 10iterations 1.809521 61.81189 at 20iterations 0.7901510 23.52834 at 30iterations 0.3450293 10.05083 at 40iterations 0.1503382 4.323897 at 50iterations 6.5673642E-02 2.050689 at 60iterations 2.8792392E-02 0.8290491 at 70iterations 1.2643543E-02 0.3934941 at 80iterations 5.5939849E-03 0.1802521 at 90iterations 2.5401760E-03 7.7487946E-02 at 100iterations 1.2165976E-03 3.8313866E-02 at 110iterations 6.4675132E-04 2.0744324E-02 at 120iterations finished qdiffx linear iterations at : 16:06:28 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 6.4675132E-04 2.0744324E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 16:06:28 7.922u 0.183s 0:08.37 96.7% 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 16:06:28 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4259 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.477651 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): 7.674000 59.37000 ymin,ymax (A): -34.39500 29.57600 zmin,zma (A): -35.37900 29.27900 x,y,z range (A): 51.69600 63.97100 64.65800 scale (grids/A): 2.477651 object centre (A): 33.52200 -2.409500 -3.050001 number of atom coordinates read : 4259 total number of charged atoms : 4108 net assigned charge : 7.500047 assigned positive charge : 635.7106 centred at (gu) : 88.41222 91.21029 95.74252 assigned negative charge : -628.2137 centred at (gu) : 87.98431 91.23272 95.83050 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 219687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35793 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105942 mr = 163734 m= 31043 mr = 84560 m= 5322 mr = 23508 m= 411 mr = 3556 m= 13 mr = 168 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 932 time to turn everything in is 1.120000 number of dielectric boundary points 86892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 32826 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) : 1.651768 object centre at (A) : 33.52200 -2.409500 -3.050001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5262336E-02 0.6178298 midg,1,midg; midg,igrid,midg 0.2745979 0.3580514 1,midg,midg; igrid,midg,midg 3.1647209E-02 0.2100024 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 1.360000 now iterating at: 16:06:30 rms-change max change #iterations 10.73575 323.0060 at 10iterations 6.270282 155.3655 at 20iterations 3.642244 72.72071 at 30iterations 2.105746 43.23240 at 40iterations 1.212891 21.77647 at 50iterations 0.6965588 12.79079 at 60iterations 0.3988948 7.368311 at 70iterations 0.2284017 3.781658 at 80iterations 0.1302203 2.616311 at 90iterations 7.4468590E-02 1.336685 at 100iterations 4.2456355E-02 0.8055019 at 110iterations 2.4162687E-02 0.4168568 at 120iterations 1.3837873E-02 0.2375469 at 130iterations 7.9329116E-03 0.1501617 at 140iterations 4.6038115E-03 8.1201553E-02 at 150iterations 2.7063699E-03 4.5381546E-02 at 160iterations 1.6435751E-03 2.9781342E-02 at 170iterations 1.0449539E-03 1.8466949E-02 at 180iterations finished qdiffx linear iterations at : 16:06:41 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.0449539E-03 1.8466949E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 16:06:42 13.161u 0.220s 0:13.66 97.9% 0+0k 0+0io 0pf+0w