Tue Oct 11 06:27:22 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 Tue Oct 11 2011 at 06:27:22 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7508806 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): 25.66400 72.07400 ymin,ymax (A): -18.71800 28.69300 zmin,zma (A): 4.018000 46.44400 x,y,z range (A): 46.41000 47.41100 42.42600 scale (grids/A): 0.7508806 object centre (A): 48.86900 4.987499 25.23100 number of atom coordinates read : 2034 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.18855 90.76353 90.16581 assigned negative charge : -304.4261 centred at (gu) : 89.33826 90.63759 90.22762 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 40448 no. pairs analyzed = 40448 no. exposed pairs = 2483 no. arc points = 17006 no. surface atoms = 848 nbur = 1186 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 612 mr = 4713 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 9.0000018E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1483 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8338 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1867604E-07 7.8872752E-08 midg,1,midg; midg,igrid,midg -2.8428276E-10 3.4657052E-07 1,midg,midg; igrid,midg,midg 3.8214878E-07 -2.5370994E-08 gauss-seidel spectral radius is 0.9907417 estimated iterations to convergence 84 setup time was (sec) 0.4800000 now iterating at: 06:27:23 rms-change max change #iterations 0.2587976 31.66236 at 10iterations 3.6384836E-02 4.527389 at 20iterations 5.3616385E-03 0.7271080 at 30iterations 9.1079529E-04 0.1111460 at 40iterations 2.2622989E-04 2.7162552E-02 at 50iterations finished qdiffx linear iterations at : 06:27:25 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.2622989E-04 2.7162552E-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) 3.280000 DelPhi exited at 06:27:27 3.288u 0.179s 0:05.14 67.1% 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 Tue Oct 11 2011 at 06:27:27 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.252642 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): 25.66400 72.07400 ymin,ymax (A): -18.71800 28.69300 zmin,zma (A): 4.018000 46.44400 x,y,z range (A): 46.41000 47.41100 42.42600 scale (grids/A): 2.252642 object centre (A): 48.86900 4.987499 25.23100 number of atom coordinates read : 2034 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 87.56557 92.29046 90.49766 assigned negative charge : -304.4261 centred at (gu) : 88.01511 91.91303 90.68297 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 83278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17006 grid for indexing accessible points = 1.400000 m= 36260 mr = 59655 m= 8164 mr = 28343 m= 940 mr = 5762 m= 38 mr = 562 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 34354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15325 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) : 0.7508806 object centre at (A) : 48.86900 4.987499 25.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4891511E-02 3.4096666E-02 midg,1,midg; midg,igrid,midg 4.4797380E-02 0.1145910 1,midg,midg; igrid,midg,midg 5.8725391E-02 -6.4809039E-02 gauss-seidel spectral radius is 0.9989393 estimated iterations to convergence 243 setup time was (sec) 0.9500000 now iterating at: 06:27:29 rms-change max change #iterations 5.020423 185.8851 at 10iterations 2.571855 87.23041 at 20iterations 1.318319 39.28963 at 30iterations 0.6778759 21.04160 at 40iterations 0.3483271 9.385895 at 50iterations 0.1784821 4.986210 at 60iterations 9.1925249E-02 2.888575 at 70iterations 4.7148556E-02 1.269180 at 80iterations 2.4444915E-02 0.7086029 at 90iterations 1.2702190E-02 0.3378811 at 100iterations 6.6175540E-03 0.2091846 at 110iterations 3.5090824E-03 9.6038818E-02 at 120iterations finished qdiffx linear iterations at : 06:27:35 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 3.5090824E-03 9.6038818E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 06:27:36 7.588u 0.236s 0:08.42 92.7% 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 Tue Oct 11 2011 at 06:27:36 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.378963 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): 25.66400 72.07400 ymin,ymax (A): -18.71800 28.69300 zmin,zma (A): 4.018000 46.44400 x,y,z range (A): 46.41000 47.41100 42.42600 scale (grids/A): 3.378963 object centre (A): 48.86900 4.987499 25.23100 number of atom coordinates read : 2034 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 86.34842 93.43562 90.74650 assigned negative charge : -304.4261 centred at (gu) : 87.02255 92.86957 91.02454 start vw surface at 0.1200000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 191202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17006 grid for indexing accessible points = 1.400000 m= 109319 mr = 142898 m= 49137 mr = 92246 m= 15953 mr = 41296 m= 3832 mr = 12872 m= 625 mr = 2945 m= 45 mr = 475 m= 0 mr = 18 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.990000 number of dielectric boundary points 77363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 15384 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) : 2.252642 object centre at (A) : 48.86900 4.987499 25.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1004308 0.2662638 midg,1,midg; midg,igrid,midg 0.3121592 0.7781742 1,midg,midg; igrid,midg,midg 0.5155900 -0.7259028 gauss-seidel spectral radius is 0.9993244 estimated iterations to convergence 303 setup time was (sec) 2.300000 now iterating at: 06:27:38 rms-change max change #iterations 10.90685 250.6695 at 10iterations 6.526215 118.1112 at 20iterations 3.899203 69.59193 at 30iterations 2.322824 43.37472 at 40iterations 1.384580 23.98425 at 50iterations 0.8223122 15.31146 at 60iterations 0.4869310 8.266666 at 70iterations 0.2893247 5.733829 at 80iterations 0.1719726 2.897751 at 90iterations 0.1020247 1.868973 at 100iterations 6.0620282E-02 1.002983 at 110iterations 3.6249720E-02 0.6167297 at 120iterations 2.1862874E-02 0.3991051 at 130iterations 1.3425208E-02 0.2257233 at 140iterations 8.4942756E-03 0.1621933 at 150iterations 5.6510959E-03 0.1068649 at 160iterations 3.9334409E-03 7.4081421E-02 at 170iterations 2.9141789E-03 5.3451538E-02 at 180iterations finished qdiffx linear iterations at : 06:27:50 total time elapsed so far: 13.98000 # loops : 180 mean,max change (kT/e) : 2.9141789E-03 5.3451538E-02 energy calculations done at 13.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.15000 DelPhi exited at 06:27:51 14.150u 0.224s 0:14.96 96.0% 0+0k 0+0io 0pf+0w