Sat Oct 8 18:53:22 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 18:53:22 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 = 2592 !!! 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: 0.6246929 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): -31.38200 17.48400 ymin,ymax (A): -23.65400 23.07100 zmin,zma (A): -12.69600 44.29200 x,y,z range (A): 48.86600 46.72500 56.98800 scale (grids/A): 0.6246929 object centre (A): -6.949000 -0.2915001 15.79800 number of atom coordinates read : 2592 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 88.45371 89.26449 89.96078 assigned negative charge : -390.0706 centred at (gu) : 88.34607 89.30382 89.85737 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6672 nv = 96 ne = 84 npr = 53653 no. pairs analyzed = 53653 no. exposed pairs = 3018 no. arc points = 21355 no. surface atoms = 1014 nbur = 1578 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3784 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.3700000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2138 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7134575E-09 1.1985119E-08 midg,1,midg; midg,igrid,midg 8.5423579E-09 1.1216524E-09 1,midg,midg; igrid,midg,midg -5.7917173E-09 8.8687910E-09 gauss-seidel spectral radius is 0.9867244 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 18:53:23 rms-change max change #iterations 0.1351506 20.62078 at 10iterations 1.2653406E-02 2.539200 at 20iterations 1.1841791E-03 0.1892529 at 30iterations 1.0934051E-04 1.7133713E-02 at 40iterations 1.0416475E-05 1.4781952E-03 at 50iterations finished qdiffx linear iterations at : 18:53:26 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.0416475E-05 1.4781952E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 18:53:27 4.074u 0.250s 0:04.75 90.9% 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 Sat Oct 8 2011 at 18:53:27 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 = 2592 !!! 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: 1.874079 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): -31.38200 17.48400 ymin,ymax (A): -23.65400 23.07100 zmin,zma (A): -12.69600 44.29200 x,y,z range (A): 48.86600 46.72500 56.98800 scale (grids/A): 1.874079 object centre (A): -6.949000 -0.2915001 15.79800 number of atom coordinates read : 2592 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 85.36068 87.79311 89.88189 assigned negative charge : -390.0706 centred at (gu) : 85.03805 87.91118 89.57178 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72634 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21355 grid for indexing accessible points = 1.400000 m= 25827 mr = 51178 m= 3877 mr = 19450 m= 249 mr = 2534 m= 4 mr = 87 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 5828 time to turn everything in is 0.6400000 number of dielectric boundary points 29343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19315 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) : 0.6246929 object centre at (A) : -6.949000 -0.2915001 15.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3959010E-02 3.0827004E-02 midg,1,midg; midg,igrid,midg 1.1902836E-02 6.4600230E-04 1,midg,midg; igrid,midg,midg -3.3559456E-05 3.3928573E-02 gauss-seidel spectral radius is 0.9985884 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 18:53:28 rms-change max change #iterations 4.121777 164.9653 at 10iterations 1.900970 63.95002 at 20iterations 0.8807085 28.92423 at 30iterations 0.4059631 13.41727 at 40iterations 0.1882264 6.051611 at 50iterations 8.7077349E-02 3.240316 at 60iterations 4.0230535E-02 1.444105 at 70iterations 1.8621620E-02 0.5654058 at 80iterations 8.6389342E-03 0.2730865 at 90iterations 3.9900718E-03 0.1293869 at 100iterations 1.8511604E-03 6.0024261E-02 at 110iterations 8.5745362E-04 2.9560089E-02 at 120iterations finished qdiffx linear iterations at : 18:53:36 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 8.5745362E-04 2.9560089E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 18:53:37 9.316u 0.294s 0:09.90 96.9% 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 Sat Oct 8 2011 at 18:53:37 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 = 2592 !!! 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: 2.811118 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): -31.38200 17.48400 ymin,ymax (A): -23.65400 23.07100 zmin,zma (A): -12.69600 44.29200 x,y,z range (A): 48.86600 46.72500 56.98800 scale (grids/A): 2.811118 object centre (A): -6.949000 -0.2915001 15.79800 number of atom coordinates read : 2592 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 83.04108 86.68956 89.82262 assigned negative charge : -390.0706 centred at (gu) : 82.55701 86.86665 89.35765 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 167878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21355 grid for indexing accessible points = 1.400000 m= 84942 mr = 123455 m= 29754 mr = 70475 m= 7060 mr = 24336 m= 1128 mr = 5500 m= 57 mr = 835 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 19070 time to turn everything in is 1.630000 number of dielectric boundary points 66201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 19689 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) : 1.874079 object centre at (A) : -6.949000 -0.2915001 15.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4177640E-02 0.3992788 midg,1,midg; midg,igrid,midg 0.1533099 -5.1697427E-03 1,midg,midg; igrid,midg,midg 9.6772080E-03 0.4184924 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.950000 now iterating at: 18:53:39 rms-change max change #iterations 9.614022 344.7888 at 10iterations 5.520473 155.0978 at 20iterations 3.151253 74.33408 at 30iterations 1.798751 32.17363 at 40iterations 1.027180 20.13655 at 50iterations 0.5851085 10.99893 at 60iterations 0.3333788 6.584896 at 70iterations 0.1898878 3.685441 at 80iterations 0.1081959 2.148404 at 90iterations 6.1609123E-02 1.111918 at 100iterations 3.5038147E-02 0.7006378 at 110iterations 1.9954497E-02 0.3452644 at 120iterations 1.1377565E-02 0.2168751 at 130iterations 6.4892871E-03 0.1179979 at 140iterations 3.6828208E-03 6.6497803E-02 at 150iterations 2.0976693E-03 4.8656464E-02 at 160iterations 1.1993684E-03 2.2006989E-02 at 170iterations 6.8157777E-04 1.2027740E-02 at 180iterations finished qdiffx linear iterations at : 18:53:52 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 6.8157777E-04 1.2027740E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 18:53:53 15.592u 0.289s 0:16.15 98.2% 0+0k 0+0io 0pf+0w