Tue Oct 11 03:22:12 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 Tue Oct 11 2011 at 03:22:12 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7161393 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): 18.67000 63.99800 ymin,ymax (A): -10.92900 33.91800 zmin,zma (A): 0.9409999 50.65200 x,y,z range (A): 45.32800 44.84700 49.71100 scale (grids/A): 0.7161393 object centre (A): 41.33400 11.49450 25.79650 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 266.8672 centred at (gu) : 90.86526 90.70232 89.60526 assigned negative charge : -259.8674 centred at (gu) : 90.98930 91.13364 89.63685 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6206 nv = 96 ne = 84 npr = 35490 no. pairs analyzed = 35490 no. exposed pairs = 2367 no. arc points = 16832 no. surface atoms = 792 nbur = 1005 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3250 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 111 time to turn everything in is 0.1500000 number of dielectric boundary points 3286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1429 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7769799E-08 5.5179253E-08 midg,1,midg; midg,igrid,midg 2.4527048E-07 -1.7220162E-07 1,midg,midg; igrid,midg,midg 1.1543219E-07 1.4019951E-08 gauss-seidel spectral radius is 0.9898119 estimated iterations to convergence 81 setup time was (sec) 0.3800000 now iterating at: 03:22:13 rms-change max change #iterations 0.1951019 32.73203 at 10iterations 2.3741897E-02 3.602747 at 20iterations 3.0442413E-03 0.4872379 at 30iterations 3.8270018E-04 5.4260254E-02 at 40iterations 4.6607529E-05 6.1302185E-03 at 50iterations finished qdiffx linear iterations at : 03:22:16 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 4.6607529E-05 6.1302185E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 03:22:17 3.704u 0.228s 0:04.23 92.6% 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 Oct 11 2011 at 03:22:17 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.148418 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): 18.67000 63.99800 ymin,ymax (A): -10.92900 33.91800 zmin,zma (A): 0.9409999 50.65200 x,y,z range (A): 45.32800 44.84700 49.71100 scale (grids/A): 2.148418 object centre (A): 41.33400 11.49450 25.79650 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 266.8672 centred at (gu) : 92.59602 92.10709 88.81621 assigned negative charge : -259.8674 centred at (gu) : 92.96822 93.40118 88.91091 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 24389 mr = 43364 m= 4340 mr = 18044 m= 365 mr = 2676 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2957 time to turn everything in is 0.3500000 number of dielectric boundary points 30188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12948 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) : 0.7161393 object centre at (A) : 41.33400 11.49450 25.79650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0115568E-02 5.5927080E-03 midg,1,midg; midg,igrid,midg 8.3136395E-02 -8.4812723E-02 1,midg,midg; igrid,midg,midg 2.3536965E-02 4.2102899E-02 gauss-seidel spectral radius is 0.9988337 estimated iterations to convergence 232 setup time was (sec) 0.5900000 now iterating at: 03:22:18 rms-change max change #iterations 4.317623 192.4137 at 10iterations 2.128021 103.1662 at 20iterations 1.050721 39.03923 at 30iterations 0.5217100 18.36216 at 40iterations 0.2592786 9.632387 at 50iterations 0.1281423 4.387257 at 60iterations 6.3407868E-02 1.935764 at 70iterations 3.1378221E-02 0.9889755 at 80iterations 1.5570708E-02 0.4877243 at 90iterations 7.7169682E-03 0.2469254 at 100iterations 3.8112034E-03 0.1308842 at 110iterations 1.8974047E-03 5.9485674E-02 at 120iterations finished qdiffx linear iterations at : 03:22:25 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.8974047E-03 5.9485674E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 03:22:25 8.025u 0.258s 0:08.67 95.3% 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 Oct 11 2011 at 03:22:25 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1797 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.222627 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): 18.67000 63.99800 ymin,ymax (A): -10.92900 33.91800 zmin,zma (A): 0.9409999 50.65200 x,y,z range (A): 45.32800 44.84700 49.71100 scale (grids/A): 3.222627 object centre (A): 41.33400 11.49450 25.79650 number of atom coordinates read : 1797 total number of charged atoms : 1631 net assigned charge : 7.000008 assigned positive charge : 266.8672 centred at (gu) : 93.89422 93.16089 88.22426 assigned negative charge : -259.8674 centred at (gu) : 94.45228 95.10190 88.36643 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 150431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 76808 mr = 105158 m= 29946 mr = 62439 m= 7876 mr = 24117 m= 1382 mr = 5780 m= 143 mr = 917 m= 8 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 10099 time to turn everything in is 0.9900000 number of dielectric boundary points 68107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 13048 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) : 2.148418 object centre at (A) : 41.33400 11.49450 25.79650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3023526 -7.5145975E-02 midg,1,midg; midg,igrid,midg 0.5246865 -0.9294822 1,midg,midg; igrid,midg,midg 0.1005861 0.5341024 gauss-seidel spectral radius is 0.9993091 estimated iterations to convergence 300 setup time was (sec) 1.230000 now iterating at: 03:22:27 rms-change max change #iterations 9.736774 295.8757 at 10iterations 5.797215 122.0511 at 20iterations 3.432353 70.97685 at 30iterations 2.021826 43.45420 at 40iterations 1.191848 23.02622 at 50iterations 0.7026479 13.41756 at 60iterations 0.4119638 8.127394 at 70iterations 0.2415600 4.678406 at 80iterations 0.1418444 2.639340 at 90iterations 8.3022244E-02 1.564922 at 100iterations 4.8635140E-02 0.8699532 at 110iterations 2.8451882E-02 0.5556183 at 120iterations 1.6687531E-02 0.3200865 at 130iterations 9.7715398E-03 0.1661091 at 140iterations 5.7090116E-03 9.9818230E-02 at 150iterations 3.3456190E-03 6.1210632E-02 at 160iterations 1.9548982E-03 3.3670425E-02 at 170iterations 1.1491387E-03 1.9239426E-02 at 180iterations finished qdiffx linear iterations at : 03:22:38 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 1.1491387E-03 1.9239426E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 03:22:38 12.333u 0.231s 0:12.90 97.3% 0+0k 0+0io 0pf+0w