Thu Jan 19 14:00:49 PST 2012 #!/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 Thu Jan 19 2012 at 14:00:53 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6826 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4268380 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): -5.263000 78.14100 ymin,ymax (A): -0.8630000 75.56700 zmin,zma (A): 158.4610 226.8660 x,y,z range (A): 83.40400 76.43000 68.40500 scale (grids/A): 0.4268380 object centre (A): 36.43900 37.35200 192.6635 number of atom coordinates read : 6826 total number of charged atoms : 6656 net assigned charge : 3.200033 assigned positive charge : 1038.346 centred at (gu) : 88.63844 89.89174 89.65936 assigned negative charge : -1035.154 centred at (gu) : 88.62840 89.95216 89.64044 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7277 nv = 96 ne = 84 npr = 136739 no. pairs analyzed = 136739 no. exposed pairs = 8970 no. arc points = 61183 no. surface atoms = 3016 nbur = 3810 mkacc time = 0.2400000 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 = 1.960000 m= 197 mr = 3371 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5020 ## 1065 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10186 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0205814E-13 1.3605193E-12 midg,1,midg; midg,igrid,midg 3.7620193E-12 -2.5375774E-12 1,midg,midg; igrid,midg,midg 8.2382518E-15 6.9381615E-13 gauss-seidel spectral radius is 0.9721568 estimated iterations to convergence 50 setup time was (sec) 0.6500000 now iterating at: 14:00:57 rms-change max change #iterations 2.9398246E-02 7.466109 at 10iterations 1.9792556E-03 0.3167830 at 20iterations 7.2050106E-04 0.1316161 at 30iterations 2.9558520E-04 5.4227829E-02 at 40iterations 1.2082140E-04 2.2095203E-02 at 50iterations finished qdiffx linear iterations at : 14:01:08 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.2082140E-04 2.2095203E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 14:01:09 4.180u 0.183s 0:17.45 24.9% 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 Thu Jan 19 2012 at 14:01:15 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6826 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.280514 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): -5.263000 78.14100 ymin,ymax (A): -0.8630000 75.56700 zmin,zma (A): 158.4610 226.8660 x,y,z range (A): 83.40400 76.43000 68.40500 scale (grids/A): 1.280514 object centre (A): 36.43900 37.35200 192.6635 number of atom coordinates read : 6826 total number of charged atoms : 6656 net assigned charge : 3.200033 assigned positive charge : 1038.346 centred at (gu) : 85.91315 89.67381 88.97626 assigned negative charge : -1035.154 centred at (gu) : 85.88525 89.85621 88.92075 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 86101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61183 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 19642 mr = 56547 m= 907 mr = 11275 m= 8 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.4700000 number of dielectric boundary points 38633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1160 ## 38 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 45901 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) : 0.4268380 object centre at (A) : 36.43900 37.35200 192.6635 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6664360E-04 -4.5545885E-06 midg,1,midg; midg,igrid,midg 2.0196473E-03 -3.6317867E-03 1,midg,midg; igrid,midg,midg 2.7907863E-03 2.8371615E-03 gauss-seidel spectral radius is 0.9973649 estimated iterations to convergence 155 setup time was (sec) 0.7300000 now iterating at: 14:01:20 rms-change max change #iterations 3.005549 133.7068 at 10iterations 1.048473 39.57392 at 20iterations 0.3661581 13.97914 at 30iterations 0.1282072 4.413052 at 40iterations 4.4781554E-02 1.566839 at 50iterations 1.5779296E-02 0.5998764 at 60iterations 5.6081237E-03 0.2079692 at 70iterations 2.1120410E-03 7.5338364E-02 at 80iterations 9.2055381E-04 3.7078857E-02 at 90iterations 5.0838117E-04 1.9872665E-02 at 100iterations 3.3453980E-04 1.3052464E-02 at 110iterations 2.3356157E-04 8.5134506E-03 at 120iterations finished qdiffx linear iterations at : 14:01:44 total time elapsed so far: 8.590000 # loops : 120 mean,max change (kT/e) : 2.3356157E-04 8.5134506E-03 energy calculations done at 8.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 14:01:45 8.730u 0.234s 0:30.76 29.1% 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 Thu Jan 19 2012 at 14:01:47 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6826 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.920771 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): -5.263000 78.14100 ymin,ymax (A): -0.8630000 75.56700 zmin,zma (A): 158.4610 226.8660 x,y,z range (A): 83.40400 76.43000 68.40500 scale (grids/A): 1.920771 object centre (A): 36.43900 37.35200 192.6635 number of atom coordinates read : 6826 total number of charged atoms : 6656 net assigned charge : 3.200033 assigned positive charge : 1038.346 centred at (gu) : 83.86948 89.51011 88.46378 assigned negative charge : -1035.154 centred at (gu) : 83.82761 89.78426 88.38125 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 202465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61183 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 76639 mr = 141786 m= 13147 mr = 55583 m= 902 mr = 8068 m= 14 mr = 321 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 2148 time to turn everything in is 1.090000 number of dielectric boundary points 87409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 52450 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) : 1.280514 object centre at (A) : 36.43900 37.35200 192.6635 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9104196E-03 -4.3671848E-03 midg,1,midg; midg,igrid,midg 2.9383574E-02 -5.8920953E-02 1,midg,midg; igrid,midg,midg 0.1579329 0.1272175 gauss-seidel spectral radius is 0.9989694 estimated iterations to convergence 246 setup time was (sec) 1.380000 now iterating at: 14:01:54 rms-change max change #iterations 9.311732 408.4993 at 10iterations 5.012900 127.8374 at 20iterations 2.680258 67.98846 at 30iterations 1.420873 33.77231 at 40iterations 0.7515604 17.08663 at 50iterations 0.3949695 9.441864 at 60iterations 0.2076845 4.726772 at 70iterations 0.1090771 2.529410 at 80iterations 5.7201345E-02 1.375179 at 90iterations 2.9812736E-02 0.6981049 at 100iterations 1.5570455E-02 0.3362217 at 110iterations 8.1418548E-03 0.1892967 at 120iterations 4.2585419E-03 8.8493347E-02 at 130iterations 2.2362620E-03 4.6855927E-02 at 140iterations 1.1783328E-03 2.5224686E-02 at 150iterations 6.3168781E-04 1.3819218E-02 at 160iterations 3.4760291E-04 7.2097778E-03 at 170iterations 2.0207535E-04 4.7359467E-03 at 180iterations finished qdiffx linear iterations at : 14:02:33 total time elapsed so far: 14.48000 # loops : 180 mean,max change (kT/e) : 2.0207535E-04 4.7359467E-03 energy calculations done at 14.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.61000 DelPhi exited at 14:02:36 14.610u 0.235s 0:49.67 29.8% 0+0k 0+0io 0pf+0w