Sat Oct 8 12:26:31 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 12:26:31 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3030 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: 0.5363950 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): -56.64800 9.721000 ymin,ymax (A): -38.14900 18.01200 zmin,zma (A): -4.229000 54.70700 x,y,z range (A): 66.36900 56.16100 58.93600 scale (grids/A): 0.5363950 object centre (A): -23.46350 -10.06850 25.23900 number of atom coordinates read : 3030 total number of charged atoms : 2892 net assigned charge : 1.000009 assigned positive charge : 417.6833 centred at (gu) : 92.60569 89.66811 89.56919 assigned negative charge : -416.6843 centred at (gu) : 92.47187 89.60341 89.53341 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6014 nv = 96 ne = 84 npr = 60722 no. pairs analyzed = 60722 no. exposed pairs = 4518 no. arc points = 32472 no. surface atoms = 1499 nbur = 1531 mkacc time = 9.9999994E-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 = 1.596000 m= 250 mr = 2589 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3089 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4157399E-10 1.6181478E-10 midg,1,midg; midg,igrid,midg -2.7476668E-10 2.7838462E-10 1,midg,midg; igrid,midg,midg -2.8773947E-10 1.1623882E-09 gauss-seidel spectral radius is 0.9821157 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 12:26:32 rms-change max change #iterations 6.2706046E-02 11.67188 at 10iterations 5.8051068E-03 1.147549 at 20iterations 1.7907583E-03 0.4012642 at 30iterations 7.2141719E-04 0.1632690 at 40iterations 2.9372834E-04 6.6699982E-02 at 50iterations finished qdiffx linear iterations at : 12:26:35 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.9372834E-04 6.6699982E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 12:26:35 3.603u 0.182s 0:04.07 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 Sat Oct 8 2011 at 12:26:35 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3030 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: 1.609185 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): -56.64800 9.721000 ymin,ymax (A): -38.14900 18.01200 zmin,zma (A): -4.229000 54.70700 x,y,z range (A): 66.36900 56.16100 58.93600 scale (grids/A): 1.609185 object centre (A): -23.46350 -10.06850 25.23900 number of atom coordinates read : 3030 total number of charged atoms : 2892 net assigned charge : 1.000009 assigned positive charge : 417.6833 centred at (gu) : 97.81637 89.00373 88.70644 assigned negative charge : -416.6843 centred at (gu) : 97.41525 88.81000 88.60001 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18707 mr = 40256 m= 1976 mr = 11201 m= 48 mr = 799 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 34162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 22162 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) : 0.5363950 object centre at (A) : -23.46350 -10.06850 25.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9735384E-03 1.0192941E-02 midg,1,midg; midg,igrid,midg -4.0096757E-03 5.4692114E-03 1,midg,midg; igrid,midg,midg -2.1036617E-03 6.3122893E-03 gauss-seidel spectral radius is 0.9981641 estimated iterations to convergence 185 setup time was (sec) 0.5900000 now iterating at: 12:26:36 rms-change max change #iterations 3.073625 156.3437 at 10iterations 1.269253 52.41775 at 20iterations 0.5218579 19.07018 at 30iterations 0.2176435 8.966026 at 40iterations 9.0187244E-02 3.298304 at 50iterations 3.7661962E-02 1.449785 at 60iterations 1.6210163E-02 0.6479530 at 70iterations 7.4852011E-03 0.3345795 at 80iterations 3.8935898E-03 0.1857529 at 90iterations 2.3560044E-03 0.1090584 at 100iterations 1.5987519E-03 7.2647095E-02 at 110iterations 1.1373722E-03 5.1898956E-02 at 120iterations finished qdiffx linear iterations at : 12:26:44 total time elapsed so far: 8.470000 # loops : 120 mean,max change (kT/e) : 1.1373722E-03 5.1898956E-02 energy calculations done at 8.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 12:26:44 8.603u 0.245s 0:09.16 96.5% 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 12:26:44 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3030 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: 2.413777 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): -56.64800 9.721000 ymin,ymax (A): -38.14900 18.01200 zmin,zma (A): -4.229000 54.70700 x,y,z range (A): 66.36900 56.16100 58.93600 scale (grids/A): 2.413777 object centre (A): -23.46350 -10.06850 25.23900 number of atom coordinates read : 3030 total number of charged atoms : 2892 net assigned charge : 1.000009 assigned positive charge : 417.6833 centred at (gu) : 101.7244 88.50526 88.05952 assigned negative charge : -416.6843 centred at (gu) : 101.1229 88.21490 87.89997 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64202 mr = 100376 m= 18081 mr = 46385 m= 2853 mr = 12148 m= 127 mr = 1618 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 77091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 23110 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) : 1.609185 object centre at (A) : -23.46350 -10.06850 25.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3616831E-03 0.1623109 midg,1,midg; midg,igrid,midg -7.8257561E-02 8.2584649E-02 1,midg,midg; igrid,midg,midg -2.3018705E-02 9.7381510E-02 gauss-seidel spectral radius is 0.9991458 estimated iterations to convergence 270 setup time was (sec) 1.140000 now iterating at: 12:26:46 rms-change max change #iterations 8.285002 319.9513 at 10iterations 4.790075 134.5702 at 20iterations 2.735434 85.01881 at 30iterations 1.549909 38.14643 at 40iterations 0.8736632 22.24950 at 50iterations 0.4899204 11.69036 at 60iterations 0.2735927 6.286439 at 70iterations 0.1527178 3.593741 at 80iterations 8.4993690E-02 1.893631 at 90iterations 4.7274645E-02 1.051025 at 100iterations 2.6304839E-02 0.5831146 at 110iterations 1.4644615E-02 0.3118935 at 120iterations 8.1915967E-03 0.1719451 at 130iterations 4.6229637E-03 9.6603394E-02 at 140iterations 2.6668492E-03 6.1927795E-02 at 150iterations 1.6011512E-03 4.0657043E-02 at 160iterations 1.0229024E-03 2.5722504E-02 at 170iterations 7.0455909E-04 1.9191742E-02 at 180iterations finished qdiffx linear iterations at : 12:26:59 total time elapsed so far: 14.43000 # loops : 180 mean,max change (kT/e) : 7.0455909E-04 1.9191742E-02 energy calculations done at 14.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 12:27:00 14.569u 0.263s 0:15.11 98.0% 0+0k 0+0io 0pf+0w