Tue Oct 11 07:36:33 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 Tue Oct 11 2011 at 07:36:34 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 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: 0.6164609 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): 71.28800 122.6200 ymin,ymax (A): -15.85500 36.30000 zmin,zma (A): -26.49100 31.25800 x,y,z range (A): 51.33200 52.15500 57.74900 scale (grids/A): 0.6164609 object centre (A): 96.95400 10.22250 2.383499 number of atom coordinates read : 3149 total number of charged atoms : 3001 net assigned charge : 8.3744526E-06 assigned positive charge : 470.8809 centred at (gu) : 89.81525 90.23839 90.69518 assigned negative charge : -470.8820 centred at (gu) : 89.93979 90.18215 90.64966 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7793 nv = 96 ne = 84 npr = 66142 no. pairs analyzed = 66142 no. exposed pairs = 3593 no. arc points = 24559 no. surface atoms = 1236 nbur = 1913 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 355 mr = 4536 m= 0 mr = 37 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.4000000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2482 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9755 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8880365E-09 3.8006442E-09 midg,1,midg; midg,igrid,midg -3.9474211E-09 4.2401700E-09 1,midg,midg; igrid,midg,midg 9.2655581E-09 -8.8602734E-09 gauss-seidel spectral radius is 0.9864127 estimated iterations to convergence 70 setup time was (sec) 0.6700000 now iterating at: 07:36:34 rms-change max change #iterations 0.1383043 19.98227 at 10iterations 1.2923810E-02 1.699238 at 20iterations 1.3979264E-03 0.1879959 at 30iterations 2.4421283E-04 4.0842056E-02 at 40iterations 5.9021742E-05 1.0570526E-02 at 50iterations finished qdiffx linear iterations at : 07:36:38 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 5.9021742E-05 1.0570526E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 07:36:38 4.130u 0.256s 0:04.95 88.4% 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 07:36:38 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.849383 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): 71.28800 122.6200 ymin,ymax (A): -15.85500 36.30000 zmin,zma (A): -26.49100 31.25800 x,y,z range (A): 51.33200 52.15500 57.74900 scale (grids/A): 1.849383 object centre (A): 96.95400 10.22250 2.383499 number of atom coordinates read : 3149 total number of charged atoms : 3001 net assigned charge : 8.3744526E-06 assigned positive charge : 470.8809 centred at (gu) : 89.44480 90.71426 92.08447 assigned negative charge : -470.8820 centred at (gu) : 89.81915 90.54587 91.94826 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24559 grid for indexing accessible points = 1.400000 m= 30021 mr = 61789 m= 4000 mr = 22507 m= 162 mr = 2413 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3047 time to turn everything in is 0.7400000 number of dielectric boundary points 33011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23511 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) : 0.6164609 object centre at (A) : 96.95400 10.22250 2.383499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1213601E-03 5.2072117E-03 midg,1,midg; midg,igrid,midg -2.0478671E-02 -9.4517739E-03 1,midg,midg; igrid,midg,midg 2.4122594E-02 -1.7723178E-02 gauss-seidel spectral radius is 0.9986007 estimated iterations to convergence 212 setup time was (sec) 1.040000 now iterating at: 07:36:40 rms-change max change #iterations 4.465866 168.9671 at 10iterations 2.065623 65.23718 at 20iterations 0.9600078 30.74084 at 30iterations 0.4469250 13.82746 at 40iterations 0.2079451 7.042217 at 50iterations 9.6817076E-02 3.047679 at 60iterations 4.5178626E-02 1.372480 at 70iterations 2.1005394E-02 0.6541328 at 80iterations 9.8085236E-03 0.2981567 at 90iterations 4.5873257E-03 0.1377225 at 100iterations 2.1518732E-03 6.6074371E-02 at 110iterations 1.0121521E-03 3.0029297E-02 at 120iterations finished qdiffx linear iterations at : 07:36:48 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 1.0121521E-03 3.0029297E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 07:36:49 9.532u 0.303s 0:10.24 95.9% 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 07:36:49 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 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: 2.774074 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): 71.28800 122.6200 ymin,ymax (A): -15.85500 36.30000 zmin,zma (A): -26.49100 31.25800 x,y,z range (A): 51.33200 52.15500 57.74900 scale (grids/A): 2.774074 object centre (A): 96.95400 10.22250 2.383499 number of atom coordinates read : 3149 total number of charged atoms : 3001 net assigned charge : 8.3744526E-06 assigned positive charge : 470.8809 centred at (gu) : 89.16697 91.07118 93.12653 assigned negative charge : -470.8820 centred at (gu) : 89.72862 90.81873 92.92230 start vw surface at 0.1700000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 198457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24559 grid for indexing accessible points = 1.400000 m= 99639 mr = 149261 m= 33206 mr = 82990 m= 6878 mr = 26700 m= 754 mr = 5223 m= 27 mr = 486 m= 0 mr = 7 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 10162 time to turn everything in is 1.900000 number of dielectric boundary points 74294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 24006 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) : 1.849383 object centre at (A) : 96.95400 10.22250 2.383499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9679352E-02 -8.5636131E-02 midg,1,midg; midg,igrid,midg -0.2366071 -0.2074610 1,midg,midg; igrid,midg,midg 0.2464489 -0.2396802 gauss-seidel spectral radius is 0.9992521 estimated iterations to convergence 289 setup time was (sec) 2.240000 now iterating at: 07:36:51 rms-change max change #iterations 10.52997 309.8494 at 10iterations 6.137682 123.9418 at 20iterations 3.548915 80.15718 at 30iterations 2.050614 37.32227 at 40iterations 1.181574 24.74781 at 50iterations 0.6803254 12.28040 at 60iterations 0.3910024 7.370121 at 70iterations 0.2247904 4.480660 at 80iterations 0.1290936 2.293568 at 90iterations 7.4102961E-02 1.423620 at 100iterations 4.2617116E-02 0.7374382 at 110iterations 2.4418984E-02 0.4079933 at 120iterations 1.4054197E-02 0.2488556 at 130iterations 8.0766911E-03 0.1424131 at 140iterations 4.6748016E-03 7.6101303E-02 at 150iterations 2.7255246E-03 4.9905777E-02 at 160iterations 1.5990357E-03 2.8125763E-02 at 170iterations 9.5616333E-04 1.7445564E-02 at 180iterations finished qdiffx linear iterations at : 07:37:05 total time elapsed so far: 15.99000 # loops : 180 mean,max change (kT/e) : 9.5616333E-04 1.7445564E-02 energy calculations done at 15.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.17000 DelPhi exited at 07:37:06 16.167u 0.294s 0:16.78 98.0% 0+0k 0+0io 0pf+0w