Sun Oct 9 08:14:24 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 Sun Oct 9 2011 at 08:14:25 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3198 !!! WARNING: NDP 1032 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5613195 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): 6.560000 54.35200 ymin,ymax (A): -30.93400 32.48800 zmin,zma (A): 124.0080 177.1630 x,y,z range (A): 47.79200 63.42200 53.15499 scale (grids/A): 0.5613195 object centre (A): 30.45600 0.7769995 150.5855 number of atom coordinates read : 3198 total number of charged atoms : 3058 net assigned charge : 7.000024 assigned positive charge : 478.8521 centred at (gu) : 91.01047 89.87212 88.75079 assigned negative charge : -471.8532 centred at (gu) : 91.03777 89.77682 88.76288 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6520 nv = 96 ne = 84 npr = 65287 no. pairs analyzed = 65287 no. exposed pairs = 4036 no. arc points = 28166 no. surface atoms = 1338 nbur = 1860 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 = 1.512000 m= 276 mr = 3372 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3300000 number of dielectric boundary points 3409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2821 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2542368E-09 4.7678883E-10 midg,1,midg; midg,igrid,midg -4.1550918E-10 1.8829340E-09 1,midg,midg; igrid,midg,midg 8.8106855E-10 5.6207122E-10 gauss-seidel spectral radius is 0.9836452 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 08:14:25 rms-change max change #iterations 8.8911742E-02 14.57264 at 10iterations 6.4811544E-03 1.164845 at 20iterations 5.2255945E-04 7.3767662E-02 at 30iterations 8.0701429E-05 1.2362719E-02 at 40iterations 2.3038827E-05 3.4117699E-03 at 50iterations finished qdiffx linear iterations at : 08:14:28 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.3038827E-05 3.4117699E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 08:14:28 3.444u 0.211s 0:03.93 92.8% 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 Sun Oct 9 2011 at 08:14:29 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3198 !!! WARNING: NDP 1032 has a net charge of -3.0000 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: 1.683958 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): 6.560000 54.35200 ymin,ymax (A): -30.93400 32.48800 zmin,zma (A): 124.0080 177.1630 x,y,z range (A): 47.79200 63.42200 53.15499 scale (grids/A): 1.683958 object centre (A): 30.45600 0.7769995 150.5855 number of atom coordinates read : 3198 total number of charged atoms : 3058 net assigned charge : 7.000024 assigned positive charge : 478.8521 centred at (gu) : 93.03094 89.61559 86.25173 assigned negative charge : -471.8532 centred at (gu) : 93.11334 89.33022 86.28844 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28166 grid for indexing accessible points = 1.400000 m= 23154 mr = 48806 m= 2603 mr = 15891 m= 76 mr = 1286 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1920 time to turn everything in is 0.5400000 number of dielectric boundary points 31647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 23577 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) : 0.5613195 object centre at (A) : 30.45600 0.7769995 150.5855 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1457633E-03 2.9092059E-03 midg,1,midg; midg,igrid,midg 1.1283475E-03 1.8338826E-02 1,midg,midg; igrid,midg,midg 6.0717119E-03 6.2163686E-03 gauss-seidel spectral radius is 0.9983238 estimated iterations to convergence 194 setup time was (sec) 0.8400000 now iterating at: 08:14:30 rms-change max change #iterations 3.704236 156.6746 at 10iterations 1.593721 58.07532 at 20iterations 0.6885445 23.23077 at 30iterations 0.2967722 10.22337 at 40iterations 0.1281155 4.529103 at 50iterations 5.5416625E-02 2.134588 at 60iterations 2.3920240E-02 0.8737431 at 70iterations 1.0366143E-02 0.3483982 at 80iterations 4.4753198E-03 0.1612167 at 90iterations 1.9470362E-03 6.3331604E-02 at 100iterations 8.5533224E-04 3.1143188E-02 at 110iterations 3.7902629E-04 1.3549805E-02 at 120iterations finished qdiffx linear iterations at : 08:14:36 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 3.7902629E-04 1.3549805E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 08:14:37 7.760u 0.228s 0:08.34 95.6% 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 Sun Oct 9 2011 at 08:14:37 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3198 !!! WARNING: NDP 1032 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.525938 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): 6.560000 54.35200 ymin,ymax (A): -30.93400 32.48800 zmin,zma (A): 124.0080 177.1630 x,y,z range (A): 47.79200 63.42200 53.15499 scale (grids/A): 2.525938 object centre (A): 30.45600 0.7769995 150.5855 number of atom coordinates read : 3198 total number of charged atoms : 3058 net assigned charge : 7.000024 assigned positive charge : 478.8521 centred at (gu) : 94.54608 89.42323 84.37746 assigned negative charge : -471.8532 centred at (gu) : 94.67001 88.99525 84.43248 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28166 grid for indexing accessible points = 1.400000 m= 77917 mr = 119408 m= 24050 mr = 61312 m= 4259 mr = 18065 m= 317 mr = 2807 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 6399 time to turn everything in is 1.260000 number of dielectric boundary points 71338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 24449 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) : 1.683958 object centre at (A) : 30.45600 0.7769995 150.5855 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8063987E-04 2.3427820E-02 midg,1,midg; midg,igrid,midg -7.7136800E-02 0.1321410 1,midg,midg; igrid,midg,midg 7.3705345E-02 0.1012268 gauss-seidel spectral radius is 0.9991887 estimated iterations to convergence 277 setup time was (sec) 1.590000 now iterating at: 08:14:39 rms-change max change #iterations 9.450279 290.7355 at 10iterations 5.433957 135.1467 at 20iterations 3.110727 70.40611 at 30iterations 1.775171 45.37678 at 40iterations 1.007428 21.08178 at 50iterations 0.5684286 11.62756 at 60iterations 0.3217119 6.768867 at 70iterations 0.1812675 3.519386 at 80iterations 0.1020854 2.165569 at 90iterations 5.7447817E-02 1.314453 at 100iterations 3.2292008E-02 0.6670380 at 110iterations 1.8141024E-02 0.3606725 at 120iterations 1.0202467E-02 0.2133484 at 130iterations 5.7175849E-03 0.1136737 at 140iterations 3.2147786E-03 6.0684204E-02 at 150iterations 1.7992074E-03 3.5503387E-02 at 160iterations 1.0101914E-03 1.9340515E-02 at 170iterations 5.6642300E-04 1.1743546E-02 at 180iterations finished qdiffx linear iterations at : 08:14:50 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 5.6642300E-04 1.1743546E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 08:14:51 12.736u 0.300s 0:13.69 95.1% 0+0k 0+0io 0pf+0w