Mon Oct 10 19:50:00 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+sph.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 = amb.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 19:50:00 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 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: 0.6193674 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): -11.98100 45.49700 ymin,ymax (A): -17.18700 36.43100 zmin,zma (A): -11.97100 45.37600 x,y,z range (A): 57.47800 53.61800 57.34700 scale (grids/A): 0.6193674 object centre (A): 16.75800 9.622000 16.70250 number of atom coordinates read : 2607 total number of charged atoms : 2469 net assigned charge : -1.999986 assigned positive charge : 385.3589 centred at (gu) : 89.65052 90.38142 90.41024 assigned negative charge : -387.3599 centred at (gu) : 89.66673 90.42857 90.37116 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6826 nv = 96 ne = 84 npr = 51768 no. pairs analyzed = 51768 no. exposed pairs = 3619 no. arc points = 25895 no. surface atoms = 1203 nbur = 1404 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 3332 m= 6 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2583 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8268 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7818881E-09 1.0543336E-09 midg,1,midg; midg,igrid,midg 1.3470329E-09 -5.0812941E-09 1,midg,midg; igrid,midg,midg -5.6357363E-10 -2.4461650E-09 gauss-seidel spectral radius is 0.9865172 estimated iterations to convergence 71 setup time was (sec) 0.7400000 now iterating at: 19:50:01 rms-change max change #iterations 0.1205136 18.17524 at 10iterations 1.1047159E-02 1.741572 at 20iterations 9.9908793E-04 0.1436501 at 30iterations 9.1444628E-05 1.3136864E-02 at 40iterations 8.5442261E-06 1.1949539E-03 at 50iterations finished qdiffx linear iterations at : 19:50:05 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 8.5442261E-06 1.1949539E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 19:50:06 4.530u 0.397s 0:05.38 91.4% 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 19:50:06 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 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: 1.858102 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): -11.98100 45.49700 ymin,ymax (A): -17.18700 36.43100 zmin,zma (A): -11.97100 45.37600 x,y,z range (A): 57.47800 53.61800 57.34700 scale (grids/A): 1.858102 object centre (A): 16.75800 9.622000 16.70250 number of atom coordinates read : 2607 total number of charged atoms : 2469 net assigned charge : -1.999986 assigned positive charge : 385.3589 centred at (gu) : 88.95121 91.14376 91.22993 assigned negative charge : -387.3599 centred at (gu) : 88.99995 91.28551 91.11329 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 73220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25895 grid for indexing accessible points = 1.400000 m= 25275 mr = 47593 m= 4008 mr = 17527 m= 240 mr = 2245 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 35313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 19329 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) : 0.6193674 object centre at (A) : 16.75800 9.622000 16.70250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6179767E-02 -3.4353402E-02 midg,1,midg; midg,igrid,midg 1.8168941E-02 -1.5595651E-03 1,midg,midg; igrid,midg,midg 1.4977647E-02 -5.0744792E-03 gauss-seidel spectral radius is 0.9985931 estimated iterations to convergence 211 setup time was (sec) 1.080000 now iterating at: 19:50:07 rms-change max change #iterations 4.034336 194.8128 at 10iterations 1.851360 61.81936 at 20iterations 0.8555623 31.11108 at 30iterations 0.3939753 13.02742 at 40iterations 0.1816527 6.011184 at 50iterations 8.3936229E-02 2.999440 at 60iterations 3.8847659E-02 1.177717 at 70iterations 1.7957715E-02 0.5503998 at 80iterations 8.3097061E-03 0.2756310 at 90iterations 3.8357847E-03 0.1258011 at 100iterations 1.7679802E-03 6.0043335E-02 at 110iterations 8.2025741E-04 2.6855946E-02 at 120iterations finished qdiffx linear iterations at : 19:50:17 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 8.2025741E-04 2.6855946E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 19:50:17 10.665u 0.449s 0:11.41 97.2% 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 19:50:17 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 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: 2.787153 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): -11.98100 45.49700 ymin,ymax (A): -17.18700 36.43100 zmin,zma (A): -11.97100 45.37600 x,y,z range (A): 57.47800 53.61800 57.34700 scale (grids/A): 2.787153 object centre (A): 16.75800 9.622000 16.70250 number of atom coordinates read : 2607 total number of charged atoms : 2469 net assigned charge : -1.999986 assigned positive charge : 385.3589 centred at (gu) : 88.42675 91.71552 91.84476 assigned negative charge : -387.3599 centred at (gu) : 88.50002 91.92832 91.66995 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 169216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25895 grid for indexing accessible points = 1.400000 m= 81424 mr = 116545 m= 29407 mr = 63885 m= 7139 mr = 22596 m= 958 mr = 4958 m= 48 mr = 511 m= 0 mr = 12 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 79685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 19751 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) : 1.858102 object centre at (A) : 16.75800 9.622000 16.70250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1127447 -0.3580841 midg,1,midg; midg,igrid,midg 0.2467012 0.1368848 1,midg,midg; igrid,midg,midg 0.2008983 -8.0966488E-02 gauss-seidel spectral radius is 0.9992600 estimated iterations to convergence 290 setup time was (sec) 2.330000 now iterating at: 19:50:20 rms-change max change #iterations 9.801684 405.0892 at 10iterations 5.800573 147.3502 at 20iterations 3.399594 86.19921 at 30iterations 1.981756 43.95884 at 40iterations 1.152978 25.70708 at 50iterations 0.6683471 14.01680 at 60iterations 0.3860266 7.617265 at 70iterations 0.2228944 4.376173 at 80iterations 0.1284453 2.470982 at 90iterations 7.4159987E-02 1.752223 at 100iterations 4.2637508E-02 0.8033047 at 110iterations 2.4547169E-02 0.4528885 at 120iterations 1.4118191E-02 0.2604637 at 130iterations 8.1079248E-03 0.1574745 at 140iterations 4.6583870E-03 8.6448669E-02 at 150iterations 2.6767075E-03 4.6459198E-02 at 160iterations 1.5392785E-03 2.7732849E-02 at 170iterations 8.8343292E-04 1.8363953E-02 at 180iterations finished qdiffx linear iterations at : 19:50:35 total time elapsed so far: 17.58000 # loops : 180 mean,max change (kT/e) : 8.8343292E-04 1.8363953E-02 energy calculations done at 17.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.80000 DelPhi exited at 19:50:36 17.806u 0.481s 0:18.75 97.4% 0+0k 0+0io 0pf+0w