Mon Oct 10 17:00:31 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 Mon Oct 10 2011 at 17:00:31 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2831 !!! WARNING: HIT 107 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: 0.6017274 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): -27.05700 32.10600 ymin,ymax (A): -11.82500 38.80200 zmin,zma (A): 5.665000 60.18400 x,y,z range (A): 59.16300 50.62700 54.51900 scale (grids/A): 0.6017274 object centre (A): 2.524500 13.48850 32.92450 number of atom coordinates read : 2831 total number of charged atoms : 2690 net assigned charge : -3.485969 assigned positive charge : 428.5272 centred at (gu) : 91.00122 90.98768 91.43674 assigned negative charge : -432.0143 centred at (gu) : 91.09264 90.87118 91.51153 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 56968 no. pairs analyzed = 56968 no. exposed pairs = 3806 no. arc points = 26235 no. surface atoms = 1269 nbur = 1562 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3468 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2100000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2748 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8499 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1592040E-09 -6.5908234E-09 midg,1,midg; midg,igrid,midg -5.2464801E-09 4.2679305E-09 1,midg,midg; igrid,midg,midg 1.8392650E-09 -6.8742585E-09 gauss-seidel spectral radius is 0.9857280 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 17:00:32 rms-change max change #iterations 0.1127221 19.79816 at 10iterations 9.6478648E-03 1.356916 at 20iterations 8.2376529E-04 0.1208649 at 30iterations 7.0027578E-05 9.2737675E-03 at 40iterations 6.2327013E-06 9.0694427E-04 at 50iterations finished qdiffx linear iterations at : 17:00:34 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 6.2327013E-06 9.0694427E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:00:35 3.443u 0.236s 0:04.29 85.5% 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 Mon Oct 10 2011 at 17:00:35 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2831 !!! WARNING: HIT 107 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: 1.805182 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): -27.05700 32.10600 ymin,ymax (A): -11.82500 38.80200 zmin,zma (A): 5.665000 60.18400 x,y,z range (A): 59.16300 50.62700 54.51900 scale (grids/A): 1.805182 object centre (A): 2.524500 13.48850 32.92450 number of atom coordinates read : 2831 total number of charged atoms : 2690 net assigned charge : -3.485969 assigned positive charge : 428.5272 centred at (gu) : 93.00302 92.96230 94.30948 assigned negative charge : -432.0143 centred at (gu) : 93.27784 92.61327 94.53432 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26235 grid for indexing accessible points = 1.400000 m= 23752 mr = 48713 m= 3061 mr = 16284 m= 135 mr = 1484 m= 0 mr = 29 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 322 time to turn everything in is 0.3700000 number of dielectric boundary points 33482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21023 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) : 0.6017274 object centre at (A) : 2.524500 13.48850 32.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1189067E-02 -1.5953942E-03 midg,1,midg; midg,igrid,midg -1.9223973E-02 3.0447610E-04 1,midg,midg; igrid,midg,midg 1.6636949E-02 -4.9243208E-02 gauss-seidel spectral radius is 0.9985077 estimated iterations to convergence 205 setup time was (sec) 0.6300000 now iterating at: 17:00:36 rms-change max change #iterations 4.011506 205.6121 at 10iterations 1.801729 65.91125 at 20iterations 0.8132374 26.96172 at 30iterations 0.3660983 13.30141 at 40iterations 0.1659327 5.361397 at 50iterations 7.4808069E-02 2.532655 at 60iterations 3.3688772E-02 1.138146 at 70iterations 1.5281501E-02 0.5165958 at 80iterations 6.8785907E-03 0.2204943 at 90iterations 3.1049731E-03 9.8171234E-02 at 100iterations 1.4105444E-03 4.7164917E-02 at 110iterations 6.3758413E-04 1.9386292E-02 at 120iterations finished qdiffx linear iterations at : 17:00:44 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 6.3758413E-04 1.9386292E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 17:00:45 8.362u 0.247s 0:09.57 89.8% 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 17:00:45 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2831 !!! WARNING: HIT 107 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: 2.707773 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): -27.05700 32.10600 ymin,ymax (A): -11.82500 38.80200 zmin,zma (A): 5.665000 60.18400 x,y,z range (A): 59.16300 50.62700 54.51900 scale (grids/A): 2.707773 object centre (A): 2.524500 13.48850 32.92450 number of atom coordinates read : 2831 total number of charged atoms : 2690 net assigned charge : -3.485969 assigned positive charge : 428.5272 centred at (gu) : 94.50427 94.44328 96.46398 assigned negative charge : -432.0143 centred at (gu) : 94.91666 93.91976 96.80148 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 169116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26235 grid for indexing accessible points = 1.400000 m= 79677 mr = 119084 m= 25361 mr = 62572 m= 4941 mr = 19060 m= 523 mr = 3174 m= 20 mr = 259 m= 0 mr = 1 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1113 time to turn everything in is 0.9400000 number of dielectric boundary points 75488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 21516 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) : 1.805182 object centre at (A) : 2.524500 13.48850 32.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3379202E-02 0.1101821 midg,1,midg; midg,igrid,midg -0.1908869 -2.6676590E-02 1,midg,midg; igrid,midg,midg 0.2089581 -0.6317719 gauss-seidel spectral radius is 0.9992379 estimated iterations to convergence 286 setup time was (sec) 1.210000 now iterating at: 17:00:46 rms-change max change #iterations 9.959487 288.6819 at 10iterations 5.860719 170.0190 at 20iterations 3.410818 92.35612 at 30iterations 1.969885 49.30987 at 40iterations 1.136637 23.34839 at 50iterations 0.6540072 12.85325 at 60iterations 0.3751774 7.965893 at 70iterations 0.2147659 3.832389 at 80iterations 0.1227076 2.302055 at 90iterations 7.0165612E-02 1.255404 at 100iterations 4.0114768E-02 0.7796611 at 110iterations 2.2837613E-02 0.4071245 at 120iterations 1.3048224E-02 0.2320237 at 130iterations 7.4352608E-03 0.1566916 at 140iterations 4.2302296E-03 7.5386047E-02 at 150iterations 2.4113725E-03 4.8233032E-02 at 160iterations 1.3749477E-03 2.4693489E-02 at 170iterations 7.8361790E-04 1.4259338E-02 at 180iterations finished qdiffx linear iterations at : 17:00:58 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 7.8361790E-04 1.4259338E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 17:00:59 13.233u 0.280s 0:13.98 96.6% 0+0k 0+0io 0pf+0w