Mon Oct 10 17:05:18 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 Mon Oct 10 2011 at 17:05:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6528756 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): 25.85200 76.90100 ymin,ymax (A): 7.921999 56.10100 zmin,zma (A): -11.64800 42.88000 x,y,z range (A): 51.04900 48.17900 54.52800 scale (grids/A): 0.6528756 object centre (A): 51.37650 32.01150 15.61600 number of atom coordinates read : 1951 total number of charged atoms : 1819 net assigned charge : -7.499985 assigned positive charge : 278.3082 centred at (gu) : 89.61751 88.61217 87.78448 assigned negative charge : -285.8081 centred at (gu) : 89.88796 88.80769 88.21223 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5685 nv = 96 ne = 84 npr = 39784 no. pairs analyzed = 39784 no. exposed pairs = 2652 no. arc points = 19303 no. surface atoms = 897 nbur = 1054 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 266 mr = 2771 m= 0 mr = 21 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2500000 number of dielectric boundary points 3159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1840 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6593 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2570044E-08 -4.4758316E-08 midg,1,midg; midg,igrid,midg 8.3326519E-09 -3.0886007E-08 1,midg,midg; igrid,midg,midg 1.5833294E-08 -4.6813351E-08 gauss-seidel spectral radius is 0.9877943 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 17:05:19 rms-change max change #iterations 0.1409279 25.33591 at 10iterations 1.4229290E-02 2.323799 at 20iterations 1.4753873E-03 0.2390976 at 30iterations 1.5225835E-04 2.7132273E-02 at 40iterations 1.5350774E-05 2.4108887E-03 at 50iterations finished qdiffx linear iterations at : 17:05:23 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 1.5350774E-05 2.4108887E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 17:05:24 4.593u 0.410s 0:05.50 90.9% 0+0k 0+0io 6pf+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 17:05:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.958627 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): 25.85200 76.90100 ymin,ymax (A): 7.921999 56.10100 zmin,zma (A): -11.64800 42.88000 x,y,z range (A): 51.04900 48.17900 54.52800 scale (grids/A): 1.958627 object centre (A): 51.37650 32.01150 15.61600 number of atom coordinates read : 1951 total number of charged atoms : 1819 net assigned charge : -7.499985 assigned positive charge : 278.3082 centred at (gu) : 88.85281 85.83651 83.35351 assigned negative charge : -285.8081 centred at (gu) : 89.66388 86.42301 84.63670 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19303 grid for indexing accessible points = 1.400000 m= 19568 mr = 39312 m= 2690 mr = 13463 m= 154 mr = 1492 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 787 time to turn everything in is 0.5100000 number of dielectric boundary points 29187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14359 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) : 0.6528756 object centre at (A) : 51.37650 32.01150 15.61600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1652817E-02 -4.8817050E-02 midg,1,midg; midg,igrid,midg 2.7455874E-02 -1.2959143E-02 1,midg,midg; igrid,midg,midg -3.7058339E-02 -4.5435369E-02 gauss-seidel spectral radius is 0.9986486 estimated iterations to convergence 216 setup time was (sec) 0.8200000 now iterating at: 17:05:25 rms-change max change #iterations 3.755021 215.2728 at 10iterations 1.759176 66.08439 at 20iterations 0.8229455 30.01164 at 30iterations 0.3853151 14.01184 at 40iterations 0.1799013 6.224102 at 50iterations 8.4814169E-02 3.025625 at 60iterations 3.9543223E-02 1.539124 at 70iterations 1.8523121E-02 0.6758219 at 80iterations 8.6954292E-03 0.3040023 at 90iterations 4.0805107E-03 0.1382270 at 100iterations 1.9100022E-03 6.6246748E-02 at 110iterations 8.9381170E-04 3.2616615E-02 at 120iterations finished qdiffx linear iterations at : 17:05:35 total time elapsed so far: 10.60000 # loops : 120 mean,max change (kT/e) : 8.9381170E-04 3.2616615E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.78000 DelPhi exited at 17:05:36 10.788u 0.445s 0:12.05 93.1% 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 Mon Oct 10 2011 at 17:05:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.937940 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): 25.85200 76.90100 ymin,ymax (A): 7.921999 56.10100 zmin,zma (A): -11.64800 42.88000 x,y,z range (A): 51.04900 48.17900 54.52800 scale (grids/A): 2.937940 object centre (A): 51.37650 32.01150 15.61600 number of atom coordinates read : 1951 total number of charged atoms : 1819 net assigned charge : -7.499985 assigned positive charge : 278.3082 centred at (gu) : 88.27914 83.75484 80.03033 assigned negative charge : -285.8081 centred at (gu) : 89.49578 84.63450 81.95507 start vw surface at 0.1000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 141225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19303 grid for indexing accessible points = 1.400000 m= 64962 mr = 96265 m= 21449 mr = 50901 m= 4472 mr = 16360 m= 560 mr = 2996 m= 25 mr = 341 m= 0 mr = 10 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 2595 time to turn everything in is 1.350000 number of dielectric boundary points 65820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 14552 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) : 1.958627 object centre at (A) : 51.37650 32.01150 15.61600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5351437 -0.4017630 midg,1,midg; midg,igrid,midg 0.2713416 -0.1357026 1,midg,midg; igrid,midg,midg -0.5565679 -0.4648367 gauss-seidel spectral radius is 0.9992660 estimated iterations to convergence 291 setup time was (sec) 1.680000 now iterating at: 17:05:38 rms-change max change #iterations 8.828357 484.2473 at 10iterations 5.138303 159.7202 at 20iterations 2.985233 66.77687 at 30iterations 1.723575 39.80385 at 40iterations 0.9926720 21.11313 at 50iterations 0.5717952 12.10992 at 60iterations 0.3289716 6.956188 at 70iterations 0.1890654 3.611606 at 80iterations 0.1084683 2.198066 at 90iterations 6.2278006E-02 1.310655 at 100iterations 3.5851970E-02 0.7664509 at 110iterations 2.0626023E-02 0.4085937 at 120iterations 1.1811297E-02 0.2321014 at 130iterations 6.7940378E-03 0.1369705 at 140iterations 3.9020188E-03 7.3287964E-02 at 150iterations 2.2408548E-03 4.5242310E-02 at 160iterations 1.2859491E-03 2.5276184E-02 at 170iterations 7.4032746E-04 1.5073776E-02 at 180iterations finished qdiffx linear iterations at : 17:05:54 total time elapsed so far: 17.81000 # loops : 180 mean,max change (kT/e) : 7.4032746E-04 1.5073776E-02 energy calculations done at 17.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.98000 DelPhi exited at 17:05:55 17.984u 0.472s 0:18.77 98.2% 0+0k 0+0io 0pf+0w