Mon Oct 10 19:34:31 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 19:34:31 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: HIR 227 has a net charge of 0.5140 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: 0.5562761 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): -40.10700 23.89000 ymin,ymax (A): -27.14800 29.59000 zmin,zma (A): 0.8600000 63.16300 x,y,z range (A): 63.99700 56.73800 62.30300 scale (grids/A): 0.5562761 object centre (A): -8.108500 1.221001 32.01150 number of atom coordinates read : 2631 total number of charged atoms : 2492 net assigned charge : 9.014030 assigned positive charge : 394.3569 centred at (gu) : 90.61136 89.39999 87.50484 assigned negative charge : -385.3440 centred at (gu) : 90.72522 89.33300 87.47151 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5421 nv = 96 ne = 84 npr = 50878 no. pairs analyzed = 50878 no. exposed pairs = 3665 no. arc points = 27423 no. surface atoms = 1221 nbur = 1410 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 232 mr = 2482 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2811 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0153932E-09 6.2367439E-10 midg,1,midg; midg,igrid,midg 3.2160954E-10 1.2116140E-09 1,midg,midg; igrid,midg,midg 1.5366896E-09 -1.4236511E-10 gauss-seidel spectral radius is 0.9833193 estimated iterations to convergence 64 setup time was (sec) 0.8300000 now iterating at: 19:34:32 rms-change max change #iterations 7.3177248E-02 12.43842 at 10iterations 5.0702603E-03 0.8647575 at 20iterations 3.5205364E-04 5.4595947E-02 at 30iterations 2.6129732E-05 4.5051575E-03 at 40iterations 2.2449399E-06 4.0149689E-04 at 50iterations finished qdiffx linear iterations at : 19:34:39 total time elapsed so far: 7.440000 # loops : 50 mean,max change (kT/e) : 2.2449399E-06 4.0149689E-04 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 19:34:40 7.626u 0.753s 0:08.90 94.0% 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 19:34:40 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: HIR 227 has a net charge of 0.5140 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: 1.668828 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): -40.10700 23.89000 ymin,ymax (A): -27.14800 29.59000 zmin,zma (A): 0.8600000 63.16300 x,y,z range (A): 63.99700 56.73800 62.30300 scale (grids/A): 1.668828 object centre (A): -8.108500 1.221001 32.01150 number of atom coordinates read : 2631 total number of charged atoms : 2492 net assigned charge : 9.014030 assigned positive charge : 394.3569 centred at (gu) : 91.83333 88.19936 82.51411 assigned negative charge : -385.3440 centred at (gu) : 92.17593 87.99883 82.41459 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27423 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18006 mr = 36703 m= 2277 mr = 11986 m= 68 mr = 1233 m= 0 mr = 13 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.6200000 number of dielectric boundary points 29307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 19124 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) : 0.5562761 object centre at (A) : -8.108500 1.221001 32.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0300424E-02 -3.8227702E-03 midg,1,midg; midg,igrid,midg 1.9248240E-02 1.7536193E-02 1,midg,midg; igrid,midg,midg 1.6334612E-02 -6.4959964E-03 gauss-seidel spectral radius is 0.9982409 estimated iterations to convergence 189 setup time was (sec) 1.200000 now iterating at: 19:34:42 rms-change max change #iterations 3.233275 166.8443 at 10iterations 1.354609 61.55446 at 20iterations 0.5708348 22.56028 at 30iterations 0.2404000 8.783728 at 40iterations 0.1011540 3.786385 at 50iterations 4.2524114E-02 1.617798 at 60iterations 1.7981941E-02 0.6178542 at 70iterations 7.5748893E-03 0.2731342 at 80iterations 3.1943109E-03 0.1421547 at 90iterations 1.3501809E-03 5.3929269E-02 at 100iterations 5.7088048E-04 2.1090508E-02 at 110iterations 2.4090848E-04 8.7509155E-03 at 120iterations finished qdiffx linear iterations at : 19:34:59 total time elapsed so far: 18.24000 # loops : 120 mean,max change (kT/e) : 2.4090848E-04 8.7509155E-03 energy calculations done at 18.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.41000 DelPhi exited at 19:34:59 18.419u 0.848s 0:19.67 97.8% 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 19:35:00 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: HIR 227 has a net charge of 0.5140 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: 2.503242 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): -40.10700 23.89000 ymin,ymax (A): -27.14800 29.59000 zmin,zma (A): 0.8600000 63.16300 x,y,z range (A): 63.99700 56.73800 62.30300 scale (grids/A): 2.503242 object centre (A): -8.108500 1.221001 32.01150 number of atom coordinates read : 2631 total number of charged atoms : 2492 net assigned charge : 9.014030 assigned positive charge : 394.3569 centred at (gu) : 92.74991 87.29896 78.77100 assigned negative charge : -385.3440 centred at (gu) : 93.26385 86.99821 78.62178 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 136570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27423 grid for indexing accessible points = 1.400000 m= 59699 mr = 90409 m= 18988 mr = 45766 m= 3681 mr = 14249 m= 322 mr = 2552 m= 3 mr = 168 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 862 time to turn everything in is 1.490000 number of dielectric boundary points 66119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19911 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) : 1.668828 object centre at (A) : -8.108500 1.221001 32.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6924123 -7.8580908E-02 midg,1,midg; midg,igrid,midg 0.3204903 0.2172418 1,midg,midg; igrid,midg,midg 0.3191293 -0.1216641 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 2.120000 now iterating at: 19:35:02 rms-change max change #iterations 8.261250 313.0677 at 10iterations 4.627064 109.6795 at 20iterations 2.576544 60.84236 at 30iterations 1.431403 33.84098 at 40iterations 0.7926092 18.17245 at 50iterations 0.4377001 9.978701 at 60iterations 0.2423328 5.287880 at 70iterations 0.1336702 2.928638 at 80iterations 7.3772855E-02 1.781208 at 90iterations 4.0671814E-02 0.8193207 at 100iterations 2.2388130E-02 0.4504366 at 110iterations 1.2326380E-02 0.2676582 at 120iterations 6.7950585E-03 0.1486740 at 130iterations 3.7393414E-03 8.0648422E-02 at 140iterations 2.0601579E-03 4.3663025E-02 at 150iterations 1.1345515E-03 2.4006397E-02 at 160iterations 6.2366069E-04 1.3853073E-02 at 170iterations 3.4357750E-04 7.2536469E-03 at 180iterations finished qdiffx linear iterations at : 19:35:32 total time elapsed so far: 31.55000 # loops : 180 mean,max change (kT/e) : 3.4357750E-04 7.2536469E-03 energy calculations done at 31.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.74000 DelPhi exited at 19:35:33 31.741u 0.870s 0:33.30 97.9% 0+0k 0+0io 0pf+0w