Sat Oct 8 11:39:57 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 11:39:57 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIR 157 has a net charge of 0.5140 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN6 653 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: 0.6239156 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): 35.46500 92.52400 ymin,ymax (A): 35.72400 84.38800 zmin,zma (A): 20.69500 69.71400 x,y,z range (A): 57.05900 48.66400 49.01900 scale (grids/A): 0.6239156 object centre (A): 63.99450 60.05600 45.20450 number of atom coordinates read : 3275 total number of charged atoms : 3124 net assigned charge : -4.985967 assigned positive charge : 502.3024 centred at (gu) : 89.57722 89.46996 89.31232 assigned negative charge : -507.2895 centred at (gu) : 89.52287 89.65070 89.29767 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8056 nv = 96 ne = 84 npr = 70364 no. pairs analyzed = 70364 no. exposed pairs = 3538 no. arc points = 24561 no. surface atoms = 1200 nbur = 2075 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 4819 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 0.3300000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2453 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9532815E-09 -2.7305558E-09 midg,1,midg; midg,igrid,midg 1.4283998E-08 -2.0022521E-08 1,midg,midg; igrid,midg,midg -1.0843474E-08 6.0348576E-10 gauss-seidel spectral radius is 0.9867381 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 11:39:58 rms-change max change #iterations 0.1579547 19.49498 at 10iterations 1.4735479E-02 2.004750 at 20iterations 1.3777374E-03 0.2134552 at 30iterations 1.3136197E-04 1.6813278E-02 at 40iterations 1.2458262E-05 1.6174316E-03 at 50iterations finished qdiffx linear iterations at : 11:40:00 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.2458262E-05 1.6174316E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 11:40:01 3.169u 0.149s 0:03.71 88.9% 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 11:40:01 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIR 157 has a net charge of 0.5140 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN6 653 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.871747 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): 35.46500 92.52400 ymin,ymax (A): 35.72400 84.38800 zmin,zma (A): 20.69500 69.71400 x,y,z range (A): 57.05900 48.66400 49.01900 scale (grids/A): 1.871747 object centre (A): 63.99450 60.05600 45.20450 number of atom coordinates read : 3275 total number of charged atoms : 3124 net assigned charge : -4.985967 assigned positive charge : 502.3024 centred at (gu) : 88.73071 88.40878 87.93595 assigned negative charge : -507.2895 centred at (gu) : 88.56824 88.95156 87.89251 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24561 grid for indexing accessible points = 1.400000 m= 32550 mr = 63999 m= 5113 mr = 25282 m= 281 mr = 3421 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 8412 time to turn everything in is 0.6100000 number of dielectric boundary points 33147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24499 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) : 0.6239156 object centre at (A) : 63.99450 60.05600 45.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7329015E-02 -1.9376315E-02 midg,1,midg; midg,igrid,midg 2.1700179E-02 -3.8031653E-02 1,midg,midg; igrid,midg,midg -1.8097702E-02 1.5601984E-02 gauss-seidel spectral radius is 0.9986348 estimated iterations to convergence 214 setup time was (sec) 0.8900000 now iterating at: 11:40:02 rms-change max change #iterations 4.809181 182.5380 at 10iterations 2.248227 69.04836 at 20iterations 1.054928 31.61449 at 30iterations 0.4952190 14.15958 at 40iterations 0.2323513 6.350775 at 50iterations 0.1090378 3.125690 at 60iterations 5.1198013E-02 1.508018 at 70iterations 2.3977451E-02 0.7033011 at 80iterations 1.1281906E-02 0.3519764 at 90iterations 5.2885022E-03 0.1500950 at 100iterations 2.4840068E-03 7.0049286E-02 at 110iterations 1.1645856E-03 3.8223267E-02 at 120iterations finished qdiffx linear iterations at : 11:40:08 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 1.1645856E-03 3.8223267E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 11:40:09 7.220u 0.181s 0:07.75 95.4% 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 Sat Oct 8 2011 at 11:40:09 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIR 157 has a net charge of 0.5140 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN6 653 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.807620 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): 35.46500 92.52400 ymin,ymax (A): 35.72400 84.38800 zmin,zma (A): 20.69500 69.71400 x,y,z range (A): 57.05900 48.66400 49.01900 scale (grids/A): 2.807620 object centre (A): 63.99450 60.05600 45.20450 number of atom coordinates read : 3275 total number of charged atoms : 3124 net assigned charge : -4.985967 assigned positive charge : 502.3024 centred at (gu) : 88.09578 87.61278 86.90375 assigned negative charge : -507.2895 centred at (gu) : 87.85217 88.42725 86.83854 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 204258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24561 grid for indexing accessible points = 1.400000 m= 105342 mr = 154818 m= 38812 mr = 88914 m= 9311 mr = 32528 m= 1280 mr = 7219 m= 63 mr = 907 m= 0 mr = 27 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 28068 time to turn everything in is 1.510000 number of dielectric boundary points 74653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 24990 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) : 1.871747 object centre at (A) : 63.99450 60.05600 45.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2056561 -0.2648855 midg,1,midg; midg,igrid,midg 0.2824742 -0.3866463 1,midg,midg; igrid,midg,midg 0.3092304 0.1714021 gauss-seidel spectral radius is 0.9992570 estimated iterations to convergence 290 setup time was (sec) 1.800000 now iterating at: 11:40:11 rms-change max change #iterations 11.03713 417.8914 at 10iterations 6.407259 110.6620 at 20iterations 3.689767 65.71137 at 30iterations 2.132212 36.02474 at 40iterations 1.225672 20.87705 at 50iterations 0.7035756 12.10870 at 60iterations 0.4048147 7.026190 at 70iterations 0.2318319 3.766766 at 80iterations 0.1331733 2.257069 at 90iterations 7.6272853E-02 1.328880 at 100iterations 4.3809786E-02 0.7445641 at 110iterations 2.5150785E-02 0.4017639 at 120iterations 1.4415242E-02 0.2251021 at 130iterations 8.2880370E-03 0.1416016 at 140iterations 4.7548390E-03 7.7699661E-02 at 150iterations 2.7284927E-03 4.4509649E-02 at 160iterations 1.5661821E-03 2.5979996E-02 at 170iterations 8.9967658E-04 1.4684200E-02 at 180iterations finished qdiffx linear iterations at : 11:40:21 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 8.9967658E-04 1.4684200E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 11:40:22 12.282u 0.208s 0:12.83 97.2% 0+0k 0+0io 0pf+0w