Sat Oct 8 15:54:47 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 8 2011 at 15:54:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6491020 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): -2.388000 45.54000 ymin,ymax (A): -14.86300 29.80200 zmin,zma (A): -19.21200 35.63300 x,y,z range (A): 47.92800 44.66500 54.84500 scale (grids/A): 0.6491020 object centre (A): 21.57600 7.469500 8.210502 number of atom coordinates read : 2255 total number of charged atoms : 2190 net assigned charge : 2.806002 assigned positive charge : 337.1492 centred at (gu) : 90.58264 88.30666 90.23159 assigned negative charge : -334.3438 centred at (gu) : 90.63433 88.44666 90.31153 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6503 nv = 96 ne = 84 npr = 44833 no. pairs analyzed = 44833 no. exposed pairs = 2893 no. arc points = 20058 no. surface atoms = 992 nbur = 1263 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3545 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2900000 number of dielectric boundary points 3284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1969 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7743 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4436957E-08 -5.5875802E-09 midg,1,midg; midg,igrid,midg 3.2617805E-08 -9.0998409E-09 1,midg,midg; igrid,midg,midg 1.0264040E-08 -1.8945776E-09 gauss-seidel spectral radius is 0.9876739 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 15:54:48 rms-change max change #iterations 0.1411740 21.43162 at 10iterations 1.4377348E-02 2.113527 at 20iterations 1.5868017E-03 0.2757492 at 30iterations 2.2782657E-04 3.1718254E-02 at 40iterations 5.4041408E-05 7.4663162E-03 at 50iterations finished qdiffx linear iterations at : 15:54:53 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 5.4041408E-05 7.4663162E-03 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.260000 DelPhi exited at 15:54:53 5.269u 0.444s 0:05.97 95.4% 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 8 2011 at 15:54:53 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.947306 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): -2.388000 45.54000 ymin,ymax (A): -14.86300 29.80200 zmin,zma (A): -19.21200 35.63300 x,y,z range (A): 47.92800 44.66500 54.84500 scale (grids/A): 1.947306 object centre (A): 21.57600 7.469500 8.210502 number of atom coordinates read : 2255 total number of charged atoms : 2190 net assigned charge : 2.806002 assigned positive charge : 337.1492 centred at (gu) : 91.74735 84.91952 90.69414 assigned negative charge : -334.3438 centred at (gu) : 91.90274 85.33984 90.93446 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20058 grid for indexing accessible points = 1.400000 m= 25723 mr = 48691 m= 4491 mr = 18869 m= 271 mr = 2879 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 0.6000000 number of dielectric boundary points 30199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17280 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) : 0.6491020 object centre at (A) : 21.57600 7.469500 8.210502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9258685E-02 -1.0311070E-02 midg,1,midg; midg,igrid,midg 2.3985809E-02 -6.7569655E-03 1,midg,midg; igrid,midg,midg 2.7823665E-03 -4.0679820E-02 gauss-seidel spectral radius is 0.9986614 estimated iterations to convergence 217 setup time was (sec) 0.9500000 now iterating at: 15:54:54 rms-change max change #iterations 4.093163 159.5633 at 10iterations 1.928876 71.35153 at 20iterations 0.9113702 27.61995 at 30iterations 0.4315463 14.88612 at 40iterations 0.2032814 6.208157 at 50iterations 9.6083470E-02 3.151620 at 60iterations 4.5326177E-02 1.377904 at 70iterations 2.1427371E-02 0.8050461 at 80iterations 1.0160027E-02 0.3116003 at 90iterations 4.8054932E-03 0.1591520 at 100iterations 2.2886053E-03 6.9522858E-02 at 110iterations 1.0885869E-03 3.4370422E-02 at 120iterations finished qdiffx linear iterations at : 15:55:06 total time elapsed so far: 12.66000 # loops : 120 mean,max change (kT/e) : 1.0885869E-03 3.4370422E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 15:55:07 12.851u 0.517s 0:13.70 97.5% 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 8 2011 at 15:55:07 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.920959 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): -2.388000 45.54000 ymin,ymax (A): -14.86300 29.80200 zmin,zma (A): -19.21200 35.63300 x,y,z range (A): 47.92800 44.66500 54.84500 scale (grids/A): 2.920959 object centre (A): 21.57600 7.469500 8.210502 number of atom coordinates read : 2255 total number of charged atoms : 2190 net assigned charge : 2.806002 assigned positive charge : 337.1492 centred at (gu) : 92.62105 82.37917 91.04112 assigned negative charge : -334.3438 centred at (gu) : 92.85416 83.00983 91.40176 start vw surface at 0.1000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 162571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20058 grid for indexing accessible points = 1.400000 m= 82214 mr = 118148 m= 31120 mr = 67025 m= 8161 mr = 24918 m= 1235 mr = 6265 m= 66 mr = 833 m= 0 mr = 19 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2509 time to turn everything in is 1.550000 number of dielectric boundary points 68159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 17520 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) : 1.947306 object centre at (A) : 21.57600 7.469500 8.210502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3051625 -5.3108215E-02 midg,1,midg; midg,igrid,midg 0.1489352 -0.1001959 1,midg,midg; igrid,midg,midg 3.0961100E-02 -0.5232424 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.960000 now iterating at: 15:55:09 rms-change max change #iterations 9.673076 518.3396 at 10iterations 5.712419 130.7760 at 20iterations 3.359436 88.66034 at 30iterations 1.964735 42.38370 at 40iterations 1.147107 24.35645 at 50iterations 0.6672857 13.21379 at 60iterations 0.3880041 7.871323 at 70iterations 0.2249469 4.185072 at 80iterations 0.1303777 2.426401 at 90iterations 7.5459689E-02 1.348951 at 100iterations 4.3662347E-02 0.7979098 at 110iterations 2.5171056E-02 0.4917145 at 120iterations 1.4561966E-02 0.2601016 at 130iterations 8.3942804E-03 0.1655388 at 140iterations 4.8479722E-03 8.5815430E-02 at 150iterations 2.7955519E-03 5.2088737E-02 at 160iterations 1.6183206E-03 3.4764290E-02 at 170iterations 9.3430647E-04 1.6567230E-02 at 180iterations finished qdiffx linear iterations at : 15:55:29 total time elapsed so far: 21.44000 # loops : 180 mean,max change (kT/e) : 9.3430647E-04 1.6567230E-02 energy calculations done at 21.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.61000 DelPhi exited at 15:55:29 21.619u 0.542s 0:22.44 98.7% 0+0k 0+0io 0pf+0w