Mon Oct 10 14:09:02 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 14:09:02 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 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: 0.6309819 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): -48.57500 7.845000 ymin,ymax (A): -58.41500 -4.709000 zmin,zma (A): -5.821000 47.06800 x,y,z range (A): 56.42000 53.70600 52.88900 scale (grids/A): 0.6309819 object centre (A): -20.36500 -31.56200 20.62350 number of atom coordinates read : 2763 total number of charged atoms : 2627 net assigned charge : -0.9999919 assigned positive charge : 425.1524 centred at (gu) : 90.83395 91.67878 90.79115 assigned negative charge : -426.1532 centred at (gu) : 90.93893 91.63918 90.74708 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7482 nv = 96 ne = 84 npr = 55136 no. pairs analyzed = 55136 no. exposed pairs = 3545 no. arc points = 24744 no. surface atoms = 1203 nbur = 1560 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4048 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3300000 number of dielectric boundary points 3794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2388 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8940 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6507744E-09 3.8700754E-09 midg,1,midg; midg,igrid,midg -3.5311234E-09 4.1012438E-09 1,midg,midg; igrid,midg,midg 7.6437017E-09 -1.4047002E-08 gauss-seidel spectral radius is 0.9870088 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 14:09:03 rms-change max change #iterations 0.1411476 20.37519 at 10iterations 1.3407749E-02 1.957504 at 20iterations 1.3364120E-03 0.1896706 at 30iterations 1.3092997E-04 1.7044067E-02 at 40iterations 1.2713889E-05 1.8749237E-03 at 50iterations finished qdiffx linear iterations at : 14:09:06 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.2713889E-05 1.8749237E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 14:09:07 3.527u 0.175s 0:04.42 83.4% 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 Mon Oct 10 2011 at 14:09:07 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 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: 1.892946 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): -48.57500 7.845000 ymin,ymax (A): -58.41500 -4.709000 zmin,zma (A): -5.821000 47.06800 x,y,z range (A): 56.42000 53.70600 52.88900 scale (grids/A): 1.892946 object centre (A): -20.36500 -31.56200 20.62350 number of atom coordinates read : 2763 total number of charged atoms : 2627 net assigned charge : -0.9999919 assigned positive charge : 425.1524 centred at (gu) : 92.50113 95.03584 92.37266 assigned negative charge : -426.1532 centred at (gu) : 92.81644 94.91706 92.24076 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24744 grid for indexing accessible points = 1.400000 m= 28788 mr = 55841 m= 4533 mr = 21001 m= 250 mr = 2798 m= 6 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2830 time to turn everything in is 0.6200000 number of dielectric boundary points 34689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20652 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) : 0.6309819 object centre at (A) : -20.36500 -31.56200 20.62350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6091665E-02 -4.4439500E-03 midg,1,midg; midg,igrid,midg -1.9494537E-02 -2.0777678E-02 1,midg,midg; igrid,midg,midg 3.4892064E-02 7.4861883E-03 gauss-seidel spectral radius is 0.9986393 estimated iterations to convergence 215 setup time was (sec) 0.9200000 now iterating at: 14:09:08 rms-change max change #iterations 4.416582 191.0177 at 10iterations 2.059123 64.96459 at 20iterations 0.9633535 35.15479 at 30iterations 0.4512940 14.22685 at 40iterations 0.2111827 6.416737 at 50iterations 9.9008694E-02 3.138441 at 60iterations 4.6350539E-02 1.491226 at 70iterations 2.1773573E-02 0.6851044 at 80iterations 1.0199416E-02 0.3099136 at 90iterations 4.7819656E-03 0.1455708 at 100iterations 2.2381970E-03 6.8283081E-02 at 110iterations 1.0555887E-03 3.3512115E-02 at 120iterations finished qdiffx linear iterations at : 14:09:15 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.0555887E-03 3.3512115E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 14:09:15 8.010u 0.223s 0:08.70 94.5% 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 14:09:15 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.839419 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): -48.57500 7.845000 ymin,ymax (A): -58.41500 -4.709000 zmin,zma (A): -5.821000 47.06800 x,y,z range (A): 56.42000 53.70600 52.88900 scale (grids/A): 2.839419 object centre (A): -20.36500 -31.56200 20.62350 number of atom coordinates read : 2763 total number of charged atoms : 2627 net assigned charge : -0.9999919 assigned positive charge : 425.1524 centred at (gu) : 93.75151 97.55343 93.55896 assigned negative charge : -426.1532 centred at (gu) : 94.22465 97.37540 93.36115 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 187272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24744 grid for indexing accessible points = 1.400000 m= 93568 mr = 135725 m= 33551 mr = 76238 m= 8054 mr = 26734 m= 1111 mr = 6015 m= 61 mr = 703 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 9915 time to turn everything in is 1.610000 number of dielectric boundary points 78182 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 21016 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) : 1.892946 object centre at (A) : -20.36500 -31.56200 20.62350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4944321E-02 -0.1547249 midg,1,midg; midg,igrid,midg -8.7067984E-02 -0.5309555 1,midg,midg; igrid,midg,midg 0.3559245 0.1093210 gauss-seidel spectral radius is 0.9992641 estimated iterations to convergence 291 setup time was (sec) 1.940000 now iterating at: 14:09:18 rms-change max change #iterations 10.43016 401.3405 at 10iterations 6.132147 126.9613 at 20iterations 3.573842 66.68885 at 30iterations 2.075860 40.56651 at 40iterations 1.202463 24.95435 at 50iterations 0.6965212 12.35557 at 60iterations 0.4024808 7.387183 at 70iterations 0.2324114 3.980128 at 80iterations 0.1343485 2.753590 at 90iterations 7.7342689E-02 1.325861 at 100iterations 4.4558652E-02 0.8478292 at 110iterations 2.5672177E-02 0.4532356 at 120iterations 1.4771497E-02 0.2726593 at 130iterations 8.5091675E-03 0.1469746 at 140iterations 4.9019763E-03 9.5924377E-02 at 150iterations 2.8241687E-03 4.8589706E-02 at 160iterations 1.6276217E-03 2.6855469E-02 at 170iterations 9.3880610E-04 1.6759872E-02 at 180iterations finished qdiffx linear iterations at : 14:09:29 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 9.3880610E-04 1.6759872E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 14:09:29 13.333u 0.215s 0:13.92 97.2% 0+0k 0+0io 0pf+0w