Sat Oct 8 19:13:46 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 19:13:46 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6209338 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): -32.00000 18.03500 ymin,ymax (A): -24.03800 22.59700 zmin,zma (A): -12.40600 44.92700 x,y,z range (A): 50.03500 46.63500 57.33300 scale (grids/A): 0.6209338 object centre (A): -6.982500 -0.7205000 16.26050 number of atom coordinates read : 2598 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.46352 89.20866 89.82721 assigned negative charge : -390.0956 centred at (gu) : 88.34681 89.25036 89.71143 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6782 nv = 96 ne = 84 npr = 52909 no. pairs analyzed = 52909 no. exposed pairs = 3111 no. arc points = 21999 no. surface atoms = 1057 nbur = 1541 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3848 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3100000 number of dielectric boundary points 3268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2155 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8159 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3425965E-09 1.1237438E-08 midg,1,midg; midg,igrid,midg 7.9588549E-09 8.5790380E-10 1,midg,midg; igrid,midg,midg -6.0973537E-09 8.3906135E-09 gauss-seidel spectral radius is 0.9865687 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 19:13:47 rms-change max change #iterations 0.1284614 17.15054 at 10iterations 1.2022429E-02 1.621277 at 20iterations 1.1327030E-03 0.1654510 at 30iterations 1.0976190E-04 1.5357971E-02 at 40iterations 1.1270701E-05 1.8920898E-03 at 50iterations finished qdiffx linear iterations at : 19:13:49 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.1270701E-05 1.8920898E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 19:13:50 3.300u 0.191s 0:03.77 92.5% 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 19:13:50 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.862802 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): -32.00000 18.03500 ymin,ymax (A): -24.03800 22.59700 zmin,zma (A): -12.40600 44.92700 x,y,z range (A): 50.03500 46.63500 57.33300 scale (grids/A): 1.862802 object centre (A): -6.982500 -0.7205000 16.26050 number of atom coordinates read : 2598 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 85.39005 87.62558 89.48102 assigned negative charge : -390.0956 centred at (gu) : 85.04034 87.75115 89.13387 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21999 grid for indexing accessible points = 1.400000 m= 27342 mr = 50925 m= 4291 mr = 20437 m= 276 mr = 2702 m= 0 mr = 95 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2338 time to turn everything in is 0.5200000 number of dielectric boundary points 30462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19309 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) : 0.6209338 object centre at (A) : -6.982500 -0.7205000 16.26050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8964624E-02 2.7360369E-02 midg,1,midg; midg,igrid,midg 1.4573371E-02 3.5788582E-03 1,midg,midg; igrid,midg,midg -7.3700002E-03 3.8151044E-02 gauss-seidel spectral radius is 0.9985772 estimated iterations to convergence 210 setup time was (sec) 0.8200000 now iterating at: 19:13:51 rms-change max change #iterations 4.047158 155.4267 at 10iterations 1.864050 68.51015 at 20iterations 0.8589864 27.20797 at 30iterations 0.3945497 13.76552 at 40iterations 0.1822860 6.654078 at 50iterations 8.4283948E-02 2.816803 at 60iterations 3.8783733E-02 1.276012 at 70iterations 1.7888054E-02 0.5672379 at 80iterations 8.2351919E-03 0.2737236 at 90iterations 3.8086765E-03 0.1198330 at 100iterations 1.7563184E-03 5.7174683E-02 at 110iterations 8.1061444E-04 2.6842833E-02 at 120iterations finished qdiffx linear iterations at : 19:13:57 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 8.1061444E-04 2.6842833E-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) 7.420000 DelPhi exited at 19:13:58 7.422u 0.220s 0:07.91 96.5% 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 19:13:58 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.794202 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): -32.00000 18.03500 ymin,ymax (A): -24.03800 22.59700 zmin,zma (A): -12.40600 44.92700 x,y,z range (A): 50.03500 46.63500 57.33300 scale (grids/A): 2.794202 object centre (A): -6.982500 -0.7205000 16.26050 number of atom coordinates read : 2598 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 83.08501 86.43818 89.22143 assigned negative charge : -390.0956 centred at (gu) : 82.56044 86.62678 88.70074 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 168092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21999 grid for indexing accessible points = 1.400000 m= 87872 mr = 122866 m= 31957 mr = 72850 m= 7715 mr = 25824 m= 1108 mr = 5824 m= 50 mr = 745 m= 0 mr = 24 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 7938 time to turn everything in is 1.310000 number of dielectric boundary points 68661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19721 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) : 1.862802 object centre at (A) : -6.982500 -0.7205000 16.26050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1271015 0.3646201 midg,1,midg; midg,igrid,midg 0.1875365 3.1776406E-02 1,midg,midg; igrid,midg,midg -4.9810659E-02 0.4793799 gauss-seidel spectral radius is 0.9992391 estimated iterations to convergence 286 setup time was (sec) 1.620000 now iterating at: 19:14:00 rms-change max change #iterations 9.534386 333.5793 at 10iterations 5.493673 115.4842 at 20iterations 3.148910 59.77535 at 30iterations 1.800859 32.93563 at 40iterations 1.028694 19.73722 at 50iterations 0.5854843 11.86244 at 60iterations 0.3345743 6.822116 at 70iterations 0.1910546 3.552358 at 80iterations 0.1088507 2.217415 at 90iterations 6.1979871E-02 1.119577 at 100iterations 3.5258938E-02 0.6838112 at 110iterations 2.0127855E-02 0.3938408 at 120iterations 1.1446652E-02 0.2267265 at 130iterations 6.5350630E-03 0.1154442 at 140iterations 3.7159221E-03 6.8389893E-02 at 150iterations 2.1208087E-03 4.1883469E-02 at 160iterations 1.2066485E-03 2.3190498E-02 at 170iterations 6.8815384E-04 1.2364388E-02 at 180iterations finished qdiffx linear iterations at : 19:14:10 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 6.8815384E-04 1.2364388E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 19:14:11 12.106u 0.213s 0:12.59 97.7% 0+0k 0+0io 0pf+0w