Sun Oct 9 12:21:31 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+sph.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 = amb.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 Sun Oct 9 2011 at 12:21:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 0.6924184 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): -14.37900 37.03500 ymin,ymax (A): 0.8270000 44.26400 zmin,zma (A): -6.091000 43.86900 x,y,z range (A): 51.41400 43.43700 49.96000 scale (grids/A): 0.6924184 object centre (A): 11.32800 22.54550 18.88900 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 91.14735 91.16376 89.74029 assigned negative charge : -366.7136 centred at (gu) : 91.33414 91.21878 89.70543 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7521 nv = 96 ne = 84 npr = 48952 no. pairs analyzed = 48952 no. exposed pairs = 2994 no. arc points = 20747 no. surface atoms = 1005 nbur = 1411 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4155 m= 1 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1932 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8639975E-09 3.4400408E-08 midg,1,midg; midg,igrid,midg 3.5332612E-08 -1.4386003E-09 1,midg,midg; igrid,midg,midg 7.7408636E-08 -7.1757633E-08 gauss-seidel spectral radius is 0.9891625 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 12:21:32 rms-change max change #iterations 0.1992694 26.86338 at 10iterations 2.3455523E-02 3.193310 at 20iterations 2.8248872E-03 0.3712902 at 30iterations 3.8289843E-04 4.8561096E-02 at 40iterations 6.6468187E-05 1.0206223E-02 at 50iterations finished qdiffx linear iterations at : 12:21:35 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 6.6468187E-05 1.0206223E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 12:21:35 3.078u 0.134s 0:03.56 89.8% 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 Sun Oct 9 2011 at 12:21:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.077255 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): -14.37900 37.03500 ymin,ymax (A): 0.8270000 44.26400 zmin,zma (A): -6.091000 43.86900 x,y,z range (A): 51.41400 43.43700 49.96000 scale (grids/A): 2.077255 object centre (A): 11.32800 22.54550 18.88900 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 93.44133 93.49092 89.22033 assigned negative charge : -366.7136 centred at (gu) : 94.00242 93.65620 89.11608 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 80184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20747 grid for indexing accessible points = 1.400000 m= 31372 mr = 55592 m= 6265 mr = 23530 m= 592 mr = 4164 m= 22 mr = 298 m= 0 mr = 1 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 34850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18056 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) : 0.6924184 object centre at (A) : 11.32800 22.54550 18.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4505900E-02 2.0964619E-02 midg,1,midg; midg,igrid,midg 3.5174534E-02 1.5826889E-03 1,midg,midg; igrid,midg,midg 2.4012053E-02 -6.5564290E-02 gauss-seidel spectral radius is 0.9988212 estimated iterations to convergence 231 setup time was (sec) 0.9200000 now iterating at: 12:21:36 rms-change max change #iterations 4.876292 211.9352 at 10iterations 2.395961 77.60294 at 20iterations 1.191345 36.84249 at 30iterations 0.5880706 18.30670 at 40iterations 0.2912123 8.648875 at 50iterations 0.1437296 4.301689 at 60iterations 7.1371168E-02 2.211483 at 70iterations 3.5233874E-02 1.061455 at 80iterations 1.7426508E-02 0.5192451 at 90iterations 8.6451098E-03 0.2518291 at 100iterations 4.2992188E-03 0.1324234 at 110iterations 2.1473356E-03 6.6807687E-02 at 120iterations finished qdiffx linear iterations at : 12:21:42 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 2.1473356E-03 6.6807687E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.140000 DelPhi exited at 12:21:43 7.140u 0.178s 0:07.67 95.3% 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 Sun Oct 9 2011 at 12:21:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 3.115883 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): -14.37900 37.03500 ymin,ymax (A): 0.8270000 44.26400 zmin,zma (A): -6.091000 43.86900 x,y,z range (A): 51.41400 43.43700 49.96000 scale (grids/A): 3.115883 object centre (A): 11.32800 22.54550 18.88900 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 95.16189 95.23621 88.83041 assigned negative charge : -366.7136 centred at (gu) : 96.00360 95.48414 88.67407 start vw surface at 0.2400000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 185121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20747 grid for indexing accessible points = 1.400000 m= 97611 mr = 134592 m= 39996 mr = 80179 m= 11792 mr = 32875 m= 2501 mr = 9145 m= 310 mr = 1807 m= 19 mr = 166 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 78582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 18192 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) : 2.077255 object centre at (A) : 11.32800 22.54550 18.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2179892 8.9891165E-02 midg,1,midg; midg,igrid,midg 0.3081545 -0.1087312 1,midg,midg; igrid,midg,midg 0.4049418 -0.6455227 gauss-seidel spectral radius is 0.9993001 estimated iterations to convergence 298 setup time was (sec) 2.190000 now iterating at: 12:21:45 rms-change max change #iterations 11.03305 412.9720 at 10iterations 6.558840 139.9975 at 20iterations 3.885276 88.68451 at 30iterations 2.298991 46.10952 at 40iterations 1.357353 25.29846 at 50iterations 0.7983093 17.04989 at 60iterations 0.4697511 8.484957 at 70iterations 0.2755299 4.998314 at 80iterations 0.1615641 2.893887 at 90iterations 9.4832778E-02 1.694540 at 100iterations 5.5530019E-02 0.9328175 at 110iterations 3.2618519E-02 0.5242004 at 120iterations 1.9072164E-02 0.3087940 at 130iterations 1.1212979E-02 0.1974792 at 140iterations 6.6095339E-03 0.1069546 at 150iterations 3.9098440E-03 6.7649841E-02 at 160iterations 2.3364876E-03 4.3216705E-02 at 170iterations 1.4228941E-03 2.9640198E-02 at 180iterations finished qdiffx linear iterations at : 12:21:55 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 1.4228941E-03 2.9640198E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 12:21:55 11.889u 0.200s 0:12.36 97.7% 0+0k 0+0io 0pf+0w