Mon Oct 10 19:37:47 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 Mon Oct 10 2011 at 19:37:47 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2633 !!! WARNING: HIR 98 has a net charge of 0.5140 !!! WARNING: HIR 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6024708 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): -30.78200 20.21000 ymin,ymax (A): -61.78100 -2.691000 zmin,zma (A): 7.879000 63.13100 x,y,z range (A): 50.99200 59.09000 55.25200 scale (grids/A): 0.6024708 object centre (A): -5.285999 -32.23600 35.50500 number of atom coordinates read : 2633 total number of charged atoms : 2495 net assigned charge : 8.028035 assigned positive charge : 391.4237 centred at (gu) : 91.06956 87.55807 87.58331 assigned negative charge : -383.3969 centred at (gu) : 91.02718 87.52119 87.58416 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 51631 no. pairs analyzed = 51631 no. exposed pairs = 3683 no. arc points = 25661 no. surface atoms = 1244 nbur = 1389 mkacc time = 9.0000004E-02 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 = 1.456000 m= 361 mr = 3186 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2599 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7974 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3607306E-09 2.1720474E-09 midg,1,midg; midg,igrid,midg 3.8286254E-09 2.9872498E-09 1,midg,midg; igrid,midg,midg 1.6470095E-09 6.7357644E-09 gauss-seidel spectral radius is 0.9857522 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 19:37:48 rms-change max change #iterations 0.1104859 17.63722 at 10iterations 9.7868843E-03 1.455651 at 20iterations 1.0854575E-03 0.1636467 at 30iterations 2.1646191E-04 3.3336639E-02 at 40iterations 6.2066392E-05 9.1438293E-03 at 50iterations finished qdiffx linear iterations at : 19:37:51 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.2066392E-05 9.1438293E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:37:51 3.412u 0.164s 0:04.02 88.8% 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 Mon Oct 10 2011 at 19:37:51 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2633 !!! WARNING: HIR 98 has a net charge of 0.5140 !!! WARNING: HIR 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.807412 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): -30.78200 20.21000 ymin,ymax (A): -61.78100 -2.691000 zmin,zma (A): 7.879000 63.13100 x,y,z range (A): 50.99200 59.09000 55.25200 scale (grids/A): 1.807412 object centre (A): -5.285999 -32.23600 35.50500 number of atom coordinates read : 2633 total number of charged atoms : 2495 net assigned charge : 8.028035 assigned positive charge : 391.4237 centred at (gu) : 93.20782 82.67352 82.74931 assigned negative charge : -383.3969 centred at (gu) : 93.08138 82.56363 82.75253 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 grid for indexing accessible points = 1.400000 m= 23541 mr = 46319 m= 3305 mr = 15988 m= 150 mr = 1768 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 33189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19501 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) : 0.6024708 object centre at (A) : -5.285999 -32.23600 35.50500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2211069E-03 1.4768798E-02 midg,1,midg; midg,igrid,midg 3.3061367E-02 2.7389567E-02 1,midg,midg; igrid,midg,midg 2.3752464E-02 1.8289648E-02 gauss-seidel spectral radius is 0.9984961 estimated iterations to convergence 205 setup time was (sec) 0.5700000 now iterating at: 19:37:52 rms-change max change #iterations 3.849016 183.0331 at 10iterations 1.715627 69.14590 at 20iterations 0.7733654 28.57470 at 30iterations 0.3480285 12.02324 at 40iterations 0.1568378 5.128663 at 50iterations 7.0568994E-02 2.505116 at 60iterations 3.1910773E-02 1.224182 at 70iterations 1.4428461E-02 0.5044670 at 80iterations 6.5630530E-03 0.2170296 at 90iterations 2.9916347E-03 0.1012230 at 100iterations 1.4014872E-03 5.2021027E-02 at 110iterations 6.7527016E-04 2.3021698E-02 at 120iterations finished qdiffx linear iterations at : 19:37:59 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 6.7527016E-04 2.3021698E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 19:38:00 7.811u 0.207s 0:08.48 94.4% 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 Mon Oct 10 2011 at 19:38:00 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2633 !!! WARNING: HIR 98 has a net charge of 0.5140 !!! WARNING: HIR 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.711118 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): -30.78200 20.21000 ymin,ymax (A): -61.78100 -2.691000 zmin,zma (A): 7.879000 63.13100 x,y,z range (A): 50.99200 59.09000 55.25200 scale (grids/A): 2.711118 object centre (A): -5.285999 -32.23600 35.50500 number of atom coordinates read : 2633 total number of charged atoms : 2495 net assigned charge : 8.028035 assigned positive charge : 391.4237 centred at (gu) : 94.81158 79.01028 79.12376 assigned negative charge : -383.3969 centred at (gu) : 94.62203 78.84541 79.12894 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 grid for indexing accessible points = 1.400000 m= 76765 mr = 113389 m= 26027 mr = 59608 m= 5608 mr = 19804 m= 671 mr = 3844 m= 32 mr = 381 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 74825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19954 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) : 1.807412 object centre at (A) : -5.285999 -32.23600 35.50500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7047480E-02 0.2523063 midg,1,midg; midg,igrid,midg 0.5539081 0.3322718 1,midg,midg; igrid,midg,midg 0.4539470 0.1340782 gauss-seidel spectral radius is 0.9992338 estimated iterations to convergence 285 setup time was (sec) 1.130000 now iterating at: 19:38:01 rms-change max change #iterations 9.607865 312.4186 at 10iterations 5.710545 168.7752 at 20iterations 3.348989 79.03996 at 30iterations 1.953895 40.68192 at 40iterations 1.133356 26.71712 at 50iterations 0.6529070 14.01615 at 60iterations 0.3755004 9.071970 at 70iterations 0.2157481 4.677958 at 80iterations 0.1236073 2.622051 at 90iterations 7.0851147E-02 1.415489 at 100iterations 4.0508803E-02 0.8984489 at 110iterations 2.3189422E-02 0.4754858 at 120iterations 1.3321797E-02 0.3466911 at 130iterations 7.6773786E-03 0.1587524 at 140iterations 4.4528805E-03 8.5861206E-02 at 150iterations 2.6199454E-03 5.0413132E-02 at 160iterations 1.5762971E-03 3.4608841E-02 at 170iterations 9.8425488E-04 2.1541595E-02 at 180iterations finished qdiffx linear iterations at : 19:38:13 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 9.8425488E-04 2.1541595E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 19:38:13 12.646u 0.211s 0:13.31 96.5% 0+0k 0+0io 0pf+0w