Tue Oct 11 04:22:43 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 Tue Oct 11 2011 at 04:22:43 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 !!! WARNING: HIR 43 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6476024 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): -10.81700 37.49500 ymin,ymax (A): -26.20000 22.35000 zmin,zma (A): -8.756000 46.21600 x,y,z range (A): 48.31200 48.55000 54.97200 scale (grids/A): 0.6476024 object centre (A): 13.33900 -1.924999 18.73000 number of atom coordinates read : 2722 total number of charged atoms : 2574 net assigned charge : 2.514022 assigned positive charge : 414.7587 centred at (gu) : 89.89684 90.32491 91.34194 assigned negative charge : -412.2453 centred at (gu) : 89.67191 90.20412 91.35360 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7752 nv = 96 ne = 84 npr = 55340 no. pairs analyzed = 55340 no. exposed pairs = 3381 no. arc points = 23542 no. surface atoms = 1138 nbur = 1584 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4397 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3100000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2331 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8208730E-09 3.6752894E-09 midg,1,midg; midg,igrid,midg -1.3024141E-08 2.4318025E-08 1,midg,midg; igrid,midg,midg -3.1090821E-08 3.7085876E-08 gauss-seidel spectral radius is 0.9876552 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 04:22:44 rms-change max change #iterations 0.1597527 25.63035 at 10iterations 1.6488675E-02 2.561280 at 20iterations 1.7056168E-03 0.2330222 at 30iterations 1.8157401E-04 2.5279999E-02 at 40iterations 2.4222854E-05 3.7536621E-03 at 50iterations finished qdiffx linear iterations at : 04:22:48 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 2.4222854E-05 3.7536621E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 04:22:48 4.594u 0.386s 0:05.73 86.7% 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 Tue Oct 11 2011 at 04:22:49 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 !!! WARNING: HIR 43 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.942807 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): -10.81700 37.49500 ymin,ymax (A): -26.20000 22.35000 zmin,zma (A): -8.756000 46.21600 x,y,z range (A): 48.31200 48.55000 54.97200 scale (grids/A): 1.942807 object centre (A): 13.33900 -1.924999 18.73000 number of atom coordinates read : 2722 total number of charged atoms : 2574 net assigned charge : 2.514022 assigned positive charge : 414.7587 centred at (gu) : 89.68973 90.97446 94.02538 assigned negative charge : -412.2453 centred at (gu) : 89.01553 90.61235 94.06048 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23542 grid for indexing accessible points = 1.400000 m= 30827 mr = 58745 m= 4779 mr = 22844 m= 274 mr = 2966 m= 6 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 327 time to turn everything in is 0.6600000 number of dielectric boundary points 34611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20286 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) : 0.6476024 object centre at (A) : 13.33900 -1.924999 18.73000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3113717E-02 -1.4016722E-02 midg,1,midg; midg,igrid,midg -1.2719178E-02 2.5017319E-02 1,midg,midg; igrid,midg,midg -1.0739329E-02 5.9899792E-02 gauss-seidel spectral radius is 0.9987026 estimated iterations to convergence 220 setup time was (sec) 0.9600000 now iterating at: 04:22:50 rms-change max change #iterations 4.641505 188.8998 at 10iterations 2.230050 88.51910 at 20iterations 1.062057 37.14477 at 30iterations 0.5071967 14.60875 at 40iterations 0.2426948 7.804291 at 50iterations 0.1161479 3.718370 at 60iterations 5.5369224E-02 1.782780 at 70iterations 2.6592223E-02 0.8714409 at 80iterations 1.2671862E-02 0.3894119 at 90iterations 6.0559544E-03 0.1699295 at 100iterations 2.8978963E-03 8.4671974E-02 at 110iterations 1.3918761E-03 4.8206329E-02 at 120iterations finished qdiffx linear iterations at : 04:23:00 total time elapsed so far: 11.35000 # loops : 120 mean,max change (kT/e) : 1.3918761E-03 4.8206329E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 04:23:01 11.521u 0.446s 0:12.45 96.0% 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 Tue Oct 11 2011 at 04:23:01 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 !!! WARNING: HIR 43 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.914211 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): -10.81700 37.49500 ymin,ymax (A): -26.20000 22.35000 zmin,zma (A): -8.756000 46.21600 x,y,z range (A): 48.31200 48.55000 54.97200 scale (grids/A): 2.914211 object centre (A): 13.33900 -1.924999 18.73000 number of atom coordinates read : 2722 total number of charged atoms : 2574 net assigned charge : 2.514022 assigned positive charge : 414.7587 centred at (gu) : 89.53455 91.46146 96.03770 assigned negative charge : -412.2453 centred at (gu) : 88.52345 90.91843 96.09046 start vw surface at 0.1200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 192712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23542 grid for indexing accessible points = 1.400000 m= 99689 mr = 141862 m= 35936 mr = 81951 m= 8445 mr = 28938 m= 1218 mr = 6291 m= 71 mr = 823 m= 0 mr = 16 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 1.780000 number of dielectric boundary points 78190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 20592 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) : 1.942807 object centre at (A) : 13.33900 -1.924999 18.73000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3162299 5.6609858E-02 midg,1,midg; midg,igrid,midg -0.1398916 0.3117070 1,midg,midg; igrid,midg,midg -6.5900050E-02 0.5367553 gauss-seidel spectral radius is 0.9992735 estimated iterations to convergence 293 setup time was (sec) 2.120000 now iterating at: 04:23:04 rms-change max change #iterations 10.66061 469.8732 at 10iterations 6.249713 142.8103 at 20iterations 3.661672 73.84409 at 30iterations 2.133338 37.27148 at 40iterations 1.240503 27.64975 at 50iterations 0.7212957 14.94047 at 60iterations 0.4193221 8.586462 at 70iterations 0.2432669 4.806860 at 80iterations 0.1413119 2.502373 at 90iterations 8.1893116E-02 1.368368 at 100iterations 4.7408197E-02 0.8213425 at 110iterations 2.7447388E-02 0.4805746 at 120iterations 1.5921719E-02 0.2928543 at 130iterations 9.2411814E-03 0.1791019 at 140iterations 5.3621894E-03 9.2180252E-02 at 150iterations 3.1331384E-03 5.5837631E-02 at 160iterations 1.8380306E-03 3.7437439E-02 at 170iterations 1.0937006E-03 2.0551682E-02 at 180iterations finished qdiffx linear iterations at : 04:23:20 total time elapsed so far: 19.01000 # loops : 180 mean,max change (kT/e) : 1.0937006E-03 2.0551682E-02 energy calculations done at 19.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.18000 DelPhi exited at 04:23:21 19.189u 0.458s 0:20.10 97.6% 0+0k 0+0io 0pf+0w