Mon Oct 10 14:18:55 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 14:18:56 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1114 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: HIT 58 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8068354 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): 41.69700 77.66900 ymin,ymax (A): 1.044000 45.16700 zmin,zma (A): 7.087000 46.16700 x,y,z range (A): 35.97200 44.12300 39.08000 scale (grids/A): 0.8068354 object centre (A): 59.68300 23.10550 26.62700 number of atom coordinates read : 1114 total number of charged atoms : 1026 net assigned charge : 2.539003 assigned positive charge : 173.7431 centred at (gu) : 89.67461 88.07993 89.60486 assigned negative charge : -171.2040 centred at (gu) : 89.72525 88.00015 89.57720 start vw surface at 5.0000001E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 5233 nv = 96 ne = 84 npr = 20875 no. pairs analyzed = 20875 no. exposed pairs = 1550 no. arc points = 11137 no. surface atoms = 516 nbur = 598 mkacc time = 3.0000005E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 2772 m= 5 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 4.0000003E-02 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.1000000 number of dielectric boundary points 2774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 763 ## 59 charges are in solution ## iepsmp to db, and charging done at 0.1600000 number of grid points assigned charge 4830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2761880E-07 2.0987028E-07 midg,1,midg; midg,igrid,midg 2.2987122E-08 2.3241680E-07 1,midg,midg; igrid,midg,midg 2.8278251E-07 7.2305582E-08 gauss-seidel spectral radius is 0.9918835 estimated iterations to convergence 90 setup time was (sec) 0.2800000 now iterating at: 14:18:56 rms-change max change #iterations 0.2517400 39.33855 at 10iterations 3.9474547E-02 6.064548 at 20iterations 6.1723138E-03 1.134394 at 30iterations 9.6907862E-04 0.1667004 at 40iterations 1.5170538E-04 2.1636963E-02 at 50iterations finished qdiffx linear iterations at : 14:18:59 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.5170538E-04 2.1636963E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 14:19:01 3.243u 0.187s 0:04.76 71.8% 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 14:19:01 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1114 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: HIT 58 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.420506 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): 41.69700 77.66900 ymin,ymax (A): 1.044000 45.16700 zmin,zma (A): 7.087000 46.16700 x,y,z range (A): 35.97200 44.12300 39.08000 scale (grids/A): 2.420506 object centre (A): 59.68300 23.10550 26.62700 number of atom coordinates read : 1114 total number of charged atoms : 1026 net assigned charge : 2.539003 assigned positive charge : 173.7431 centred at (gu) : 89.02367 84.23991 88.81470 assigned negative charge : -171.2040 centred at (gu) : 89.17584 84.00049 88.73167 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 53121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11137 grid for indexing accessible points = 1.400000 m= 22674 mr = 34924 m= 5921 mr = 17401 m= 791 mr = 4306 m= 42 mr = 526 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.3000000 number of dielectric boundary points 25375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8193 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) : 0.8068354 object centre at (A) : 59.68300 23.10550 26.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6029130E-02 4.2289354E-02 midg,1,midg; midg,igrid,midg -1.3189510E-02 -2.4081422E-03 1,midg,midg; igrid,midg,midg 3.8050257E-02 -2.2154916E-02 gauss-seidel spectral radius is 0.9989808 estimated iterations to convergence 248 setup time was (sec) 0.5000000 now iterating at: 14:19:01 rms-change max change #iterations 4.289831 284.0387 at 10iterations 2.213846 91.09196 at 20iterations 1.144854 44.31339 at 30iterations 0.5933984 20.53023 at 40iterations 0.3077296 12.60705 at 50iterations 0.1588106 5.016634 at 60iterations 8.2533792E-02 3.023469 at 70iterations 4.2581122E-02 1.653944 at 80iterations 2.2108600E-02 0.7097626 at 90iterations 1.1437092E-02 0.3893461 at 100iterations 5.9275110E-03 0.2163277 at 110iterations 3.0637423E-03 0.1159592 at 120iterations finished qdiffx linear iterations at : 14:19:08 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 3.0637423E-03 0.1159592 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:19:09 7.562u 0.189s 0:08.16 94.8% 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 14:19:09 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1114 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: HIT 58 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.630759 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): 41.69700 77.66900 ymin,ymax (A): 1.044000 45.16700 zmin,zma (A): 7.087000 46.16700 x,y,z range (A): 35.97200 44.12300 39.08000 scale (grids/A): 3.630759 object centre (A): 59.68300 23.10550 26.62700 number of atom coordinates read : 1114 total number of charged atoms : 1026 net assigned charge : 2.539003 assigned positive charge : 173.7431 centred at (gu) : 88.53557 81.35982 88.22208 assigned negative charge : -171.2040 centred at (gu) : 88.76373 81.00078 88.09756 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 121650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11137 grid for indexing accessible points = 1.400000 m= 66262 mr = 83886 m= 32127 mr = 54941 m= 11996 mr = 27035 m= 3081 mr = 9752 m= 537 mr = 2504 m= 25 mr = 417 m= 2 mr = 10 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1182 time to turn everything in is 0.8700000 number of dielectric boundary points 57136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 8208 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) : 2.420506 object centre at (A) : 59.68300 23.10550 26.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6331956 0.3547790 midg,1,midg; midg,igrid,midg 3.5295688E-02 2.2267012E-02 1,midg,midg; igrid,midg,midg 0.2774844 -0.2856765 gauss-seidel spectral radius is 0.9993296 estimated iterations to convergence 305 setup time was (sec) 1.090000 now iterating at: 14:19:10 rms-change max change #iterations 9.081399 302.8121 at 10iterations 5.359603 121.1191 at 20iterations 3.159060 63.05517 at 30iterations 1.867330 42.18169 at 40iterations 1.097791 24.28785 at 50iterations 0.6471832 13.13040 at 60iterations 0.3818489 7.598917 at 70iterations 0.2241157 4.885459 at 80iterations 0.1323029 2.527727 at 90iterations 7.7715404E-02 1.603287 at 100iterations 4.5688815E-02 0.8741789 at 110iterations 2.6937379E-02 0.5177937 at 120iterations 1.5828071E-02 0.3184338 at 130iterations 9.3291672E-03 0.1796532 at 140iterations 5.4921359E-03 0.1109257 at 150iterations 3.2324982E-03 6.2761307E-02 at 160iterations 1.9053627E-03 3.5978317E-02 at 170iterations 1.1230675E-03 2.1833420E-02 at 180iterations finished qdiffx linear iterations at : 14:19:21 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 1.1230675E-03 2.1833420E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 14:19:22 12.273u 0.224s 0:12.83 97.3% 0+0k 0+0io 0pf+0w