Tue Nov 22 14:15:35 PST 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 Tue Nov 22 2011 at 14:15:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1989 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6038606 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 0.6038606 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 1989 total number of charged atoms : 1857 net assigned charge : 2.000005 assigned positive charge : 293.5859 centred at (gu) : 90.10554 90.05196 90.27271 assigned negative charge : -291.5863 centred at (gu) : 90.13503 90.12766 90.41082 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4904 nv = 96 ne = 84 npr = 39594 no. pairs analyzed = 39594 no. exposed pairs = 2652 no. arc points = 18121 no. surface atoms = 907 nbur = 1082 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 251 mr = 2555 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1848 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8792232E-09 -3.5647678E-09 midg,1,midg; midg,igrid,midg 3.2711007E-09 -1.3852781E-09 1,midg,midg; igrid,midg,midg 1.8549832E-09 7.7454293E-11 gauss-seidel spectral radius is 0.9857562 estimated iterations to convergence 69 setup time was (sec) 0.4400000 now iterating at: 14:15:37 rms-change max change #iterations 9.8896891E-02 19.18288 at 10iterations 8.3351871E-03 1.383792 at 20iterations 7.1800669E-04 0.1355581 at 30iterations 6.1913030E-05 1.0558844E-02 at 40iterations 5.4236498E-06 9.6321106E-04 at 50iterations finished qdiffx linear iterations at : 14:15:42 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 5.4236498E-06 9.6321106E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 14:15:43 3.166u 0.165s 0:07.70 43.1% 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 Nov 22 2011 at 14:15:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1989 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.811582 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 1.811582 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 1989 total number of charged atoms : 1857 net assigned charge : 2.000005 assigned positive charge : 293.5859 centred at (gu) : 90.31671 90.15588 90.81797 assigned negative charge : -291.5863 centred at (gu) : 90.40535 90.38317 91.23271 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18121 grid for indexing accessible points = 1.400000 m= 18989 mr = 35088 m= 2738 mr = 13820 m= 124 mr = 1599 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 23728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 14501 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) : 0.6038606 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9302986E-03 -8.4800087E-03 midg,1,midg; midg,igrid,midg 1.5962529E-03 -3.3715714E-03 1,midg,midg; igrid,midg,midg 4.2386346E-02 2.9679297E-02 gauss-seidel spectral radius is 0.9984252 estimated iterations to convergence 200 setup time was (sec) 0.6600000 now iterating at: 14:15:45 rms-change max change #iterations 3.265172 149.4205 at 10iterations 1.437657 55.04407 at 20iterations 0.6374916 25.87970 at 30iterations 0.2810078 11.67343 at 40iterations 0.1238551 5.223875 at 50iterations 5.4688323E-02 2.101516 at 60iterations 2.4268152E-02 0.9039569 at 70iterations 1.0719595E-02 0.4395415 at 80iterations 4.7619436E-03 0.1857715 at 90iterations 2.0986027E-03 8.2553864E-02 at 100iterations 9.3086693E-04 3.5243988E-02 at 110iterations 4.1296927E-04 1.5625000E-02 at 120iterations finished qdiffx linear iterations at : 14:15:57 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 4.1296927E-04 1.5625000E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 14:15:59 7.170u 0.193s 0:15.71 46.8% 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 Tue Nov 22 2011 at 14:15:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1989 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.717373 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 2.717373 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 1989 total number of charged atoms : 1857 net assigned charge : 2.000005 assigned positive charge : 293.5859 centred at (gu) : 90.47501 90.23377 91.22697 assigned negative charge : -291.5863 centred at (gu) : 90.60812 90.57478 91.84911 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 120927 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18121 grid for indexing accessible points = 1.400000 m= 60758 mr = 85041 m= 21920 mr = 49133 m= 4854 mr = 17439 m= 550 mr = 3547 m= 28 mr = 337 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 53539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 14850 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) : 1.811582 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9380405E-02 -7.7675000E-02 midg,1,midg; midg,igrid,midg -1.0849539E-02 -3.1938482E-02 1,midg,midg; igrid,midg,midg 0.4688550 0.3530422 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 1.220000 now iterating at: 14:16:01 rms-change max change #iterations 8.063088 334.8798 at 10iterations 4.660884 137.7190 at 20iterations 2.650628 69.17358 at 30iterations 1.510091 36.91003 at 40iterations 0.8505729 19.55968 at 50iterations 0.4794648 11.22642 at 60iterations 0.2703376 6.317317 at 70iterations 0.1517850 3.519220 at 80iterations 8.5178606E-02 1.885109 at 90iterations 4.7973718E-02 1.129040 at 100iterations 2.6871458E-02 0.6339678 at 110iterations 1.5033333E-02 0.3512878 at 120iterations 8.4179258E-03 0.1927423 at 130iterations 4.7118412E-03 9.5928192E-02 at 140iterations 2.6454502E-03 5.8181763E-02 at 150iterations 1.4805100E-03 3.2239914E-02 at 160iterations 8.2568481E-04 2.0636082E-02 at 170iterations 4.6113390E-04 1.0147095E-02 at 180iterations finished qdiffx linear iterations at : 14:16:21 total time elapsed so far: 11.12000 # loops : 180 mean,max change (kT/e) : 4.6113390E-04 1.0147095E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 14:16:22 11.296u 0.221s 0:22.83 50.4% 0+0k 0+0io 0pf+0w