Sat Oct 8 17:40:09 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 Sat Oct 8 2011 at 17:40:09 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3581 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ASP 451 has a net charge of -0.2720 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: 0.5243545 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): -0.2200000 45.42500 ymin,ymax (A): -30.57900 31.22800 zmin,zma (A): 1.540000 69.43300 x,y,z range (A): 45.64500 61.80700 67.89300 scale (grids/A): 0.5243545 object centre (A): 22.60250 0.3244991 35.48650 number of atom coordinates read : 3581 total number of charged atoms : 3434 net assigned charge : -5.871980 assigned positive charge : 550.0261 centred at (gu) : 90.28976 90.83755 90.69346 assigned negative charge : -555.9000 centred at (gu) : 90.24606 90.80011 90.68334 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6264 nv = 96 ne = 84 npr = 72450 no. pairs analyzed = 72450 no. exposed pairs = 4365 no. arc points = 30224 no. surface atoms = 1473 nbur = 2108 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 206 mr = 3316 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3088 ## 483 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8391 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5940561E-10 -1.3924242E-10 midg,1,midg; midg,igrid,midg -2.3288624E-10 -2.3269367E-11 1,midg,midg; igrid,midg,midg -2.8859629E-10 2.7515312E-12 gauss-seidel spectral radius is 0.9813074 estimated iterations to convergence 60 setup time was (sec) 0.7000000 now iterating at: 17:40:10 rms-change max change #iterations 6.9172800E-02 12.44549 at 10iterations 4.3182005E-03 0.6221581 at 20iterations 4.5300490E-04 8.7734222E-02 at 30iterations 1.0168836E-04 1.9458771E-02 at 40iterations 2.7083965E-05 5.0134659E-03 at 50iterations finished qdiffx linear iterations at : 17:40:14 total time elapsed so far: 5.210000 # loops : 50 mean,max change (kT/e) : 2.7083965E-05 5.0134659E-03 energy calculations done at 5.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.380000 DelPhi exited at 17:40:15 5.387u 0.468s 0:06.11 95.5% 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 Sat Oct 8 2011 at 17:40:15 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3581 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ASP 451 has a net charge of -0.2720 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: 1.573063 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): -0.2200000 45.42500 ymin,ymax (A): -30.57900 31.22800 zmin,zma (A): 1.540000 69.43300 x,y,z range (A): 45.64500 61.80700 67.89300 scale (grids/A): 1.573063 object centre (A): 22.60250 0.3244991 35.48650 number of atom coordinates read : 3581 total number of charged atoms : 3434 net assigned charge : -5.871980 assigned positive charge : 550.0261 centred at (gu) : 90.86824 92.51134 92.07906 assigned negative charge : -555.9000 centred at (gu) : 90.73788 92.39990 92.04993 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30224 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20923 mr = 48638 m= 1930 mr = 14285 m= 28 mr = 887 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 328 time to turn everything in is 0.6000000 number of dielectric boundary points 29431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 396 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 26040 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) : 0.5243545 object centre at (A) : 22.60250 0.3244991 35.48650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5471746E-03 6.5424512E-03 midg,1,midg; midg,igrid,midg -1.1144071E-02 -9.4438000E-03 1,midg,midg; igrid,midg,midg -5.3031598E-03 1.7238517E-03 gauss-seidel spectral radius is 0.9980928 estimated iterations to convergence 182 setup time was (sec) 0.9600000 now iterating at: 17:40:16 rms-change max change #iterations 3.476881 173.2399 at 10iterations 1.416006 50.40991 at 20iterations 0.5774860 21.65746 at 30iterations 0.2366512 8.538146 at 40iterations 9.6797042E-02 3.466080 at 50iterations 3.9453045E-02 1.272681 at 60iterations 1.6211880E-02 0.6094623 at 70iterations 6.6481344E-03 0.2212029 at 80iterations 2.7358702E-03 9.0555191E-02 at 90iterations 1.1346344E-03 4.4696331E-02 at 100iterations 4.7942722E-04 1.8859863E-02 at 110iterations 2.1009549E-04 7.9748631E-03 at 120iterations finished qdiffx linear iterations at : 17:40:28 total time elapsed so far: 12.28000 # loops : 120 mean,max change (kT/e) : 2.1009549E-04 7.9748631E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 17:40:28 12.540u 0.532s 0:13.32 98.1% 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 Sat Oct 8 2011 at 17:40:28 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3581 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ASP 451 has a net charge of -0.2720 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: 2.359595 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): -0.2200000 45.42500 ymin,ymax (A): -30.57900 31.22800 zmin,zma (A): 1.540000 69.43300 x,y,z range (A): 45.64500 61.80700 67.89300 scale (grids/A): 2.359595 object centre (A): 22.60250 0.3244991 35.48650 number of atom coordinates read : 3581 total number of charged atoms : 3434 net assigned charge : -5.871980 assigned positive charge : 550.0261 centred at (gu) : 91.30219 93.76685 93.11849 assigned negative charge : -555.9000 centred at (gu) : 91.10677 93.59985 93.07478 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 163987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30224 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 74263 mr = 119193 m= 19490 mr = 58680 m= 2809 mr = 14567 m= 164 mr = 1761 m= 0 mr = 49 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 994 time to turn everything in is 1.460000 number of dielectric boundary points 66463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 27407 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) : 1.573063 object centre at (A) : 22.60250 0.3244991 35.48650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2990897 3.4143303E-02 midg,1,midg; midg,igrid,midg -0.1530405 -0.1824645 1,midg,midg; igrid,midg,midg -8.6714700E-02 3.6311284E-02 gauss-seidel spectral radius is 0.9991160 estimated iterations to convergence 266 setup time was (sec) 1.870000 now iterating at: 17:40:31 rms-change max change #iterations 9.132361 293.6504 at 10iterations 5.054089 113.1056 at 20iterations 2.789833 60.50701 at 30iterations 1.534019 32.84206 at 40iterations 0.8401196 19.01432 at 50iterations 0.4610356 9.911121 at 60iterations 0.2516325 5.403256 at 70iterations 0.1375315 2.966078 at 80iterations 7.5176835E-02 1.510420 at 90iterations 4.1071985E-02 0.8591843 at 100iterations 2.2391733E-02 0.4609680 at 110iterations 1.2226801E-02 0.2635517 at 120iterations 6.6798129E-03 0.1330853 at 130iterations 3.6420431E-03 7.3841095E-02 at 140iterations 1.9897197E-03 3.9625645E-02 at 150iterations 1.0908502E-03 2.2058487E-02 at 160iterations 5.9925736E-04 1.1602402E-02 at 170iterations 3.3117755E-04 7.1430206E-03 at 180iterations finished qdiffx linear iterations at : 17:40:51 total time elapsed so far: 21.94000 # loops : 180 mean,max change (kT/e) : 3.3117755E-04 7.1430206E-03 energy calculations done at 21.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.11000 DelPhi exited at 17:40:51 22.115u 0.567s 0:22.93 98.8% 0+0k 0+0io 0pf+0w