Mon Oct 10 14:00:36 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 14:00:36 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 = 2573 !!! 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: ZN6 600 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: 0.6174338 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): -31.26400 18.18900 ymin,ymax (A): -23.57600 23.57600 zmin,zma (A): -12.58100 45.07700 x,y,z range (A): 49.45300 47.15200 57.65800 scale (grids/A): 0.6174338 object centre (A): -6.537500 0.0000000E+00 16.24800 number of atom coordinates read : 2573 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.26105 88.99470 89.62498 assigned negative charge : -390.0956 centred at (gu) : 88.16456 89.05418 89.50099 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6347 nv = 96 ne = 84 npr = 53444 no. pairs analyzed = 53444 no. exposed pairs = 2976 no. arc points = 21667 no. surface atoms = 1006 nbur = 1567 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3507 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2800000 number of dielectric boundary points 3136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2188 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7051834E-09 1.0119152E-08 midg,1,midg; midg,igrid,midg 8.8622905E-09 -1.6336998E-10 1,midg,midg; igrid,midg,midg -3.9226928E-09 6.3842260E-09 gauss-seidel spectral radius is 0.9864109 estimated iterations to convergence 70 setup time was (sec) 0.5000000 now iterating at: 14:00:37 rms-change max change #iterations 0.1256443 22.28644 at 10iterations 1.1304092E-02 1.547390 at 20iterations 1.0304997E-03 0.1446552 at 30iterations 9.7586402E-05 1.5098572E-02 at 40iterations 8.7168673E-06 1.2550354E-03 at 50iterations finished qdiffx linear iterations at : 14:00:39 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 8.7168673E-06 1.2550354E-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) 3.340000 DelPhi exited at 14:00:40 3.345u 0.143s 0:04.08 85.2% 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 14:00:40 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 = 2573 !!! 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: ZN6 600 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: 1.852301 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): -31.26400 18.18900 ymin,ymax (A): -23.57600 23.57600 zmin,zma (A): -12.58100 45.07700 x,y,z range (A): 49.45300 47.15200 57.65800 scale (grids/A): 1.852301 object centre (A): -6.537500 0.0000000E+00 16.24800 number of atom coordinates read : 2573 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 84.78254 86.98352 88.87446 assigned negative charge : -390.0956 centred at (gu) : 84.49345 87.16261 88.50269 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21667 grid for indexing accessible points = 1.400000 m= 23388 mr = 47794 m= 3330 mr = 17139 m= 154 mr = 1978 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4487 time to turn everything in is 0.4700000 number of dielectric boundary points 28974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19339 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) : 0.6174338 object centre at (A) : -6.537500 0.0000000E+00 16.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6000479E-02 3.0501850E-02 midg,1,midg; midg,igrid,midg 1.3425744E-02 6.8053935E-04 1,midg,midg; igrid,midg,midg -5.8399246E-04 3.1351916E-02 gauss-seidel spectral radius is 0.9985520 estimated iterations to convergence 208 setup time was (sec) 0.7400000 now iterating at: 14:00:41 rms-change max change #iterations 3.997686 168.5196 at 10iterations 1.828484 65.50356 at 20iterations 0.8362734 26.93153 at 30iterations 0.3831057 13.23310 at 40iterations 0.1750204 5.819313 at 50iterations 8.0582432E-02 2.580341 at 60iterations 3.6784679E-02 1.273216 at 70iterations 1.6861172E-02 0.5615540 at 80iterations 7.7131349E-03 0.2552986 at 90iterations 3.5509851E-03 0.1204357 at 100iterations 1.6217045E-03 5.0199509E-02 at 110iterations 7.4296980E-04 2.5604248E-02 at 120iterations finished qdiffx linear iterations at : 14:00:47 total time elapsed so far: 7.030000 # loops : 120 mean,max change (kT/e) : 7.4296980E-04 2.5604248E-02 energy calculations done at 7.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 14:00:48 7.209u 0.240s 0:07.80 95.3% 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 14:00:48 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 = 2573 !!! 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: ZN6 600 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: 2.778452 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): -31.26400 18.18900 ymin,ymax (A): -23.57600 23.57600 zmin,zma (A): -12.58100 45.07700 x,y,z range (A): 49.45300 47.15200 57.65800 scale (grids/A): 2.778452 object centre (A): -6.537500 0.0000000E+00 16.24800 number of atom coordinates read : 2573 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 82.17368 85.47514 88.31176 assigned negative charge : -390.0956 centred at (gu) : 81.74010 85.74386 87.75397 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21667 grid for indexing accessible points = 1.400000 m= 77890 mr = 116098 m= 26025 mr = 63772 m= 5797 mr = 20725 m= 693 mr = 4222 m= 36 mr = 435 m= 0 mr = 6 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 14849 time to turn everything in is 1.190000 number of dielectric boundary points 65347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.330000 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) : 1.852301 object centre at (A) : -6.537500 0.0000000E+00 16.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8806738E-02 0.3888973 midg,1,midg; midg,igrid,midg 0.1608848 4.9381284E-04 1,midg,midg; igrid,midg,midg 5.2392553E-03 0.3824780 gauss-seidel spectral radius is 0.9992297 estimated iterations to convergence 284 setup time was (sec) 1.500000 now iterating at: 14:00:50 rms-change max change #iterations 9.438196 295.2259 at 10iterations 5.411766 137.2491 at 20iterations 3.092451 73.14993 at 30iterations 1.763029 40.34727 at 40iterations 1.002743 21.11871 at 50iterations 0.5706398 11.86570 at 60iterations 0.3240282 6.735508 at 70iterations 0.1845098 3.867746 at 80iterations 0.1047652 1.853275 at 90iterations 5.9568293E-02 1.209225 at 100iterations 3.3781972E-02 0.6674194 at 110iterations 1.9172212E-02 0.3776474 at 120iterations 1.0907492E-02 0.2433147 at 130iterations 6.1962213E-03 0.1178875 at 140iterations 3.5203479E-03 7.1231842E-02 at 150iterations 2.0013538E-03 3.8497925E-02 at 160iterations 1.1357612E-03 2.2262573E-02 at 170iterations 6.4796791E-04 1.3702393E-02 at 180iterations finished qdiffx linear iterations at : 14:01:01 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 6.4796791E-04 1.3702393E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 14:01:02 12.584u 0.228s 0:14.04 91.1% 0+0k 0+0io 0pf+0w