Mon Oct 10 20:15:29 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 20:15:29 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 = 2593 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: 0.6266613 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): -11.91300 40.63900 ymin,ymax (A): 33.88300 87.26900 zmin,zma (A): -12.12800 44.68100 x,y,z range (A): 52.55200 53.38601 56.80900 scale (grids/A): 0.6266613 object centre (A): 14.36300 60.57600 16.27650 number of atom coordinates read : 2593 total number of charged atoms : 2458 net assigned charge : 1.9311905E-05 assigned positive charge : 382.6449 centred at (gu) : 90.66454 89.49535 89.69237 assigned negative charge : -382.6458 centred at (gu) : 90.69167 89.50563 89.79815 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6810 nv = 96 ne = 84 npr = 52360 no. pairs analyzed = 52360 no. exposed pairs = 3540 no. arc points = 25388 no. surface atoms = 1166 nbur = 1427 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 3453 m= 3 mr = 64 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 0.3100000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2384 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8693692E-09 -7.9434939E-09 midg,1,midg; midg,igrid,midg 8.9754010E-10 -7.4209178E-10 1,midg,midg; igrid,midg,midg 1.8414381E-09 -2.5205751E-09 gauss-seidel spectral radius is 0.9868195 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 20:15:30 rms-change max change #iterations 0.1324074 18.60557 at 10iterations 1.2667625E-02 1.902214 at 20iterations 1.2708450E-03 0.1697903 at 30iterations 1.7085690E-04 2.8114319E-02 at 40iterations 3.4065684E-05 6.5803528E-03 at 50iterations finished qdiffx linear iterations at : 20:15:32 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.4065684E-05 6.5803528E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 20:15:33 3.338u 0.172s 0:04.16 84.1% 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 Mon Oct 10 2011 at 20:15:33 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 = 2593 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.879984 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): -11.91300 40.63900 ymin,ymax (A): 33.88300 87.26900 zmin,zma (A): -12.12800 44.68100 x,y,z range (A): 52.55200 53.38601 56.80900 scale (grids/A): 1.879984 object centre (A): 14.36300 60.57600 16.27650 number of atom coordinates read : 2593 total number of charged atoms : 2458 net assigned charge : 1.9311905E-05 assigned positive charge : 382.6449 centred at (gu) : 91.99314 88.48527 89.07639 assigned negative charge : -382.6458 centred at (gu) : 92.07497 88.51681 89.39439 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25388 grid for indexing accessible points = 1.400000 m= 26637 mr = 47696 m= 5007 mr = 19114 m= 306 mr = 3089 m= 7 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1298 time to turn everything in is 0.5300000 number of dielectric boundary points 34367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19336 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) : 0.6266613 object centre at (A) : 14.36300 60.57600 16.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1954607E-03 -5.1345944E-02 midg,1,midg; midg,igrid,midg 3.5008904E-02 -1.0443303E-02 1,midg,midg; igrid,midg,midg 1.2214291E-02 3.3392764E-03 gauss-seidel spectral radius is 0.9986148 estimated iterations to convergence 213 setup time was (sec) 0.8100000 now iterating at: 20:15:34 rms-change max change #iterations 4.104551 195.4228 at 10iterations 1.899862 69.20882 at 20iterations 0.8836679 33.72249 at 30iterations 0.4096479 12.67585 at 40iterations 0.1905084 6.282196 at 50iterations 8.8895470E-02 2.757267 at 60iterations 4.1325212E-02 1.354637 at 70iterations 1.9305978E-02 0.6079636 at 80iterations 8.9806039E-03 0.2791204 at 90iterations 4.1857366E-03 0.1356544 at 100iterations 1.9636166E-03 6.2779427E-02 at 110iterations 9.2185783E-04 3.0360937E-02 at 120iterations finished qdiffx linear iterations at : 20:15:41 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 9.2185783E-04 3.0360937E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 20:15:41 7.437u 0.229s 0:08.33 91.8% 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 20:15:42 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 = 2593 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: 2.819976 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): -11.91300 40.63900 ymin,ymax (A): 33.88300 87.26900 zmin,zma (A): -12.12800 44.68100 x,y,z range (A): 52.55200 53.38601 56.80900 scale (grids/A): 2.819976 object centre (A): 14.36300 60.57600 16.27650 number of atom coordinates read : 2593 total number of charged atoms : 2458 net assigned charge : 1.9311905E-05 assigned positive charge : 382.6449 centred at (gu) : 92.98958 87.72778 88.61436 assigned negative charge : -382.6458 centred at (gu) : 93.11248 87.77506 89.09161 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 167234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25388 grid for indexing accessible points = 1.400000 m= 83193 mr = 116529 m= 33238 mr = 66185 m= 9117 mr = 26393 m= 1404 mr = 6690 m= 81 mr = 917 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 4462 time to turn everything in is 1.370000 number of dielectric boundary points 77527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19662 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) : 1.879984 object centre at (A) : 14.36300 60.57600 16.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2528856E-02 -0.5960949 midg,1,midg; midg,igrid,midg 0.7945716 -0.1015444 1,midg,midg; igrid,midg,midg 0.1187934 -5.3700797E-02 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.680000 now iterating at: 20:15:43 rms-change max change #iterations 9.710458 490.2856 at 10iterations 5.698520 148.7379 at 20iterations 3.316930 64.59505 at 30iterations 1.927312 37.71097 at 40iterations 1.113714 22.53473 at 50iterations 0.6455994 12.48667 at 60iterations 0.3738121 7.403439 at 70iterations 0.2148499 4.245640 at 80iterations 0.1240635 2.292732 at 90iterations 7.1493395E-02 1.324156 at 100iterations 4.1098226E-02 0.7432218 at 110iterations 2.3699572E-02 0.4471650 at 120iterations 1.3647133E-02 0.2523775 at 130iterations 7.9141976E-03 0.1458569 at 140iterations 4.5946166E-03 8.2271576E-02 at 150iterations 2.6850270E-03 4.9499512E-02 at 160iterations 1.5954309E-03 2.9283524E-02 at 170iterations 9.6288178E-04 1.8600464E-02 at 180iterations finished qdiffx linear iterations at : 20:15:54 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 9.6288178E-04 1.8600464E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 20:15:55 12.280u 0.225s 0:13.12 95.2% 0+0k 0+0io 0pf+0w