Tue Oct 11 04:48:42 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 04:48:42 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6541712 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): -12.27800 37.20400 ymin,ymax (A): -26.02100 22.58600 zmin,zma (A): -8.918000 45.50200 x,y,z range (A): 49.48200 48.60700 54.42000 scale (grids/A): 0.6541712 object centre (A): 12.46300 -1.717500 18.29200 number of atom coordinates read : 2754 total number of charged atoms : 2602 net assigned charge : 3.154013 assigned positive charge : 419.1908 centred at (gu) : 90.31306 90.54137 91.58257 assigned negative charge : -416.0373 centred at (gu) : 90.05427 90.34632 91.52601 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7946 nv = 96 ne = 84 npr = 56196 no. pairs analyzed = 56196 no. exposed pairs = 3287 no. arc points = 22934 no. surface atoms = 1117 nbur = 1637 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 4583 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3200000 number of dielectric boundary points 3741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2250 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7631273E-09 2.3187285E-08 midg,1,midg; midg,igrid,midg -2.6586768E-08 4.6157069E-08 1,midg,midg; igrid,midg,midg -3.9323620E-08 5.5786543E-08 gauss-seidel spectral radius is 0.9878999 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 04:48:43 rms-change max change #iterations 0.1679512 22.51061 at 10iterations 1.7975392E-02 2.750210 at 20iterations 1.8693175E-03 0.2531242 at 30iterations 2.0429752E-04 2.6617050E-02 at 40iterations 2.6516263E-05 4.3449402E-03 at 50iterations finished qdiffx linear iterations at : 04:48:45 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 2.6516263E-05 4.3449402E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 04:48:46 3.186u 0.161s 0:03.96 84.3% 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 04:48:46 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.962514 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): -12.27800 37.20400 ymin,ymax (A): -26.02100 22.58600 zmin,zma (A): -8.918000 45.50200 x,y,z range (A): 49.48200 48.60700 54.42000 scale (grids/A): 1.962514 object centre (A): 12.46300 -1.717500 18.29200 number of atom coordinates read : 2754 total number of charged atoms : 2602 net assigned charge : 3.154013 assigned positive charge : 419.1908 centred at (gu) : 90.93876 91.62372 94.74691 assigned negative charge : -416.0373 centred at (gu) : 90.16240 91.03876 94.57786 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22934 grid for indexing accessible points = 1.400000 m= 32235 mr = 60325 m= 5355 mr = 24475 m= 305 mr = 3459 m= 7 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1222 time to turn everything in is 0.6500000 number of dielectric boundary points 34376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20533 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) : 0.6541712 object centre at (A) : 12.46300 -1.717500 18.29200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8461693E-02 1.2914281E-02 midg,1,midg; midg,igrid,midg -1.3689506E-02 3.4888398E-02 1,midg,midg; igrid,midg,midg -1.2991042E-02 6.2820323E-02 gauss-seidel spectral radius is 0.9987244 estimated iterations to convergence 222 setup time was (sec) 0.9300000 now iterating at: 04:48:47 rms-change max change #iterations 4.738767 197.6253 at 10iterations 2.282043 71.60327 at 20iterations 1.098839 33.04766 at 30iterations 0.5294340 15.66475 at 40iterations 0.2549911 8.686083 at 50iterations 0.1231054 3.722375 at 60iterations 5.8916144E-02 1.594402 at 70iterations 2.8486026E-02 0.8151484 at 80iterations 1.3670300E-02 0.3853188 at 90iterations 6.5839100E-03 0.2024565 at 100iterations 3.1687147E-03 9.2330933E-02 at 110iterations 1.5248640E-03 4.4228554E-02 at 120iterations finished qdiffx linear iterations at : 04:48:54 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.5248640E-03 4.4228554E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 04:48:55 7.869u 0.203s 0:08.71 92.5% 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 Tue Oct 11 2011 at 04:48:55 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.943771 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): -12.27800 37.20400 ymin,ymax (A): -26.02100 22.58600 zmin,zma (A): -8.918000 45.50200 x,y,z range (A): 49.48200 48.60700 54.42000 scale (grids/A): 2.943771 object centre (A): 12.46300 -1.717500 18.29200 number of atom coordinates read : 2754 total number of charged atoms : 2602 net assigned charge : 3.154013 assigned positive charge : 419.1908 centred at (gu) : 91.40784 92.43546 97.12033 assigned negative charge : -416.0373 centred at (gu) : 90.24361 91.55824 96.86666 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 196070 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22934 grid for indexing accessible points = 1.400000 m= 102824 mr = 145476 m= 38820 mr = 85559 m= 9730 mr = 31903 m= 1424 mr = 7477 m= 97 mr = 969 m= 0 mr = 42 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 4308 time to turn everything in is 1.450000 number of dielectric boundary points 77539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 20812 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) : 1.962514 object centre at (A) : 12.46300 -1.717500 18.29200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4481119 0.3414960 midg,1,midg; midg,igrid,midg -0.1365359 0.3947415 1,midg,midg; igrid,midg,midg -9.2648163E-02 0.4750977 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 1.740000 now iterating at: 04:48:57 rms-change max change #iterations 10.84571 348.9488 at 10iterations 6.377019 151.0495 at 20iterations 3.741545 80.86834 at 30iterations 2.192522 38.76489 at 40iterations 1.280289 26.46016 at 50iterations 0.7486026 13.44255 at 60iterations 0.4361146 8.024300 at 70iterations 0.2536526 4.700042 at 80iterations 0.1477227 2.554709 at 90iterations 8.5837685E-02 1.455988 at 100iterations 4.9761415E-02 0.8027191 at 110iterations 2.8923117E-02 0.4933472 at 120iterations 1.6787520E-02 0.3063984 at 130iterations 9.7339125E-03 0.1518533 at 140iterations 5.6551490E-03 9.1373444E-02 at 150iterations 3.2825745E-03 5.5956841E-02 at 160iterations 1.9049891E-03 3.1177521E-02 at 170iterations 1.1045855E-03 1.9229889E-02 at 180iterations finished qdiffx linear iterations at : 04:49:07 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 1.1045855E-03 1.9229889E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 04:49:07 11.880u 0.188s 0:12.42 97.1% 0+0k 0+0io 0pf+0w