Tue Oct 11 03:49:05 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 03:49:05 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 0.6607766 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): -9.479000 36.59500 ymin,ymax (A): -26.88700 21.78100 zmin,zma (A): -8.257000 45.61900 x,y,z range (A): 46.07400 48.66800 53.87600 scale (grids/A): 0.6607766 object centre (A): 13.55800 -2.552999 18.68100 number of atom coordinates read : 2701 total number of charged atoms : 2616 net assigned charge : 1.926024 assigned positive charge : 424.3367 centred at (gu) : 89.37568 90.52737 91.38556 assigned negative charge : -422.4112 centred at (gu) : 89.08628 90.40132 91.38827 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8179 nv = 96 ne = 84 npr = 51561 no. pairs analyzed = 51561 no. exposed pairs = 3504 no. arc points = 24360 no. surface atoms = 1163 nbur = 1538 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4557 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3600000 number of dielectric boundary points 4022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5384136E-09 6.3545187E-09 midg,1,midg; midg,igrid,midg -2.0171280E-08 3.6487272E-08 1,midg,midg; igrid,midg,midg -6.8579062E-08 5.8666352E-08 gauss-seidel spectral radius is 0.9881427 estimated iterations to convergence 75 setup time was (sec) 0.6400000 now iterating at: 03:49:05 rms-change max change #iterations 0.1768621 26.36931 at 10iterations 1.9290633E-02 2.911926 at 20iterations 2.0870052E-03 0.2557144 at 30iterations 2.4006156E-04 3.0225754E-02 at 40iterations 3.2713910E-05 4.1046143E-03 at 50iterations finished qdiffx linear iterations at : 03:49:09 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 3.2713910E-05 4.1046143E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 03:49:10 4.175u 0.256s 0:05.14 85.9% 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 Tue Oct 11 2011 at 03:49:10 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 1.982330 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): -9.479000 36.59500 ymin,ymax (A): -26.88700 21.78100 zmin,zma (A): -8.257000 45.61900 x,y,z range (A): 46.07400 48.66800 53.87600 scale (grids/A): 1.982330 object centre (A): 13.55800 -2.552999 18.68100 number of atom coordinates read : 2701 total number of charged atoms : 2616 net assigned charge : 1.926024 assigned positive charge : 424.3367 centred at (gu) : 88.12627 91.58149 94.15639 assigned negative charge : -422.4112 centred at (gu) : 87.25867 91.20371 94.16426 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24360 grid for indexing accessible points = 1.400000 m= 34153 mr = 61316 m= 6031 mr = 25593 m= 418 mr = 3947 m= 3 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 0.7800000 number of dielectric boundary points 37195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20627 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) : 0.6607766 object centre at (A) : 13.55800 -2.552999 18.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3775094E-03 6.3037309E-03 midg,1,midg; midg,igrid,midg -2.3790158E-02 5.0553274E-03 1,midg,midg; igrid,midg,midg -3.7259538E-02 6.4206578E-02 gauss-seidel spectral radius is 0.9987552 estimated iterations to convergence 224 setup time was (sec) 1.070000 now iterating at: 03:49:11 rms-change max change #iterations 4.871297 231.0008 at 10iterations 2.372373 74.08710 at 20iterations 1.149879 32.19611 at 30iterations 0.5575331 18.39842 at 40iterations 0.2714826 7.564179 at 50iterations 0.1313878 4.069251 at 60iterations 6.3993067E-02 1.937122 at 70iterations 3.0958736E-02 0.9253244 at 80iterations 1.5013002E-02 0.4647083 at 90iterations 7.3099383E-03 0.2048073 at 100iterations 3.5445162E-03 9.5685959E-02 at 110iterations 1.7258084E-03 5.1767826E-02 at 120iterations finished qdiffx linear iterations at : 03:49:20 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 1.7258084E-03 5.1767826E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 03:49:20 9.793u 0.320s 0:10.53 96.0% 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 Tue Oct 11 2011 at 03:49:20 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2701 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.973495 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): -9.479000 36.59500 ymin,ymax (A): -26.88700 21.78100 zmin,zma (A): -8.257000 45.61900 x,y,z range (A): 46.07400 48.66800 53.87600 scale (grids/A): 2.973495 object centre (A): 13.55800 -2.552999 18.68100 number of atom coordinates read : 2701 total number of charged atoms : 2616 net assigned charge : 1.926024 assigned positive charge : 424.3367 centred at (gu) : 87.18923 92.37218 96.23454 assigned negative charge : -422.4112 centred at (gu) : 85.88795 91.80544 96.24638 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 201906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24360 grid for indexing accessible points = 1.400000 m= 107822 mr = 147768 m= 42214 mr = 89195 m= 11245 mr = 34324 m= 1860 mr = 8634 m= 139 mr = 1314 m= 6 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 1340 time to turn everything in is 2.070000 number of dielectric boundary points 83895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 20928 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) : 1.982330 object centre at (A) : 13.55800 -2.552999 18.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8112624E-03 0.2681576 midg,1,midg; midg,igrid,midg -0.2721422 5.9285939E-02 1,midg,midg; igrid,midg,midg -0.3096434 0.5694563 gauss-seidel spectral radius is 0.9992973 estimated iterations to convergence 298 setup time was (sec) 2.410000 now iterating at: 03:49:23 rms-change max change #iterations 11.27404 355.4766 at 10iterations 6.706057 145.9477 at 20iterations 3.975295 87.24348 at 30iterations 2.351809 47.45295 at 40iterations 1.386488 25.27434 at 50iterations 0.8175539 15.36889 at 60iterations 0.4804677 8.697796 at 70iterations 0.2817909 5.665381 at 80iterations 0.1651339 2.714160 at 90iterations 9.6693955E-02 1.547508 at 100iterations 5.6695029E-02 1.037210 at 110iterations 3.3140190E-02 0.5579071 at 120iterations 1.9392677E-02 0.3412476 at 130iterations 1.1326093E-02 0.2041855 at 140iterations 6.6156755E-03 0.1104507 at 150iterations 3.8700826E-03 6.3369751E-02 at 160iterations 2.2711086E-03 3.8767815E-02 at 170iterations 1.3291498E-03 2.3940563E-02 at 180iterations finished qdiffx linear iterations at : 03:49:38 total time elapsed so far: 16.77000 # loops : 180 mean,max change (kT/e) : 1.3291498E-03 2.3940563E-02 energy calculations done at 16.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 03:49:38 16.945u 0.325s 0:17.57 98.2% 0+0k 0+0io 0pf+0w