Sun Oct 9 01:47:47 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 Sun Oct 9 2011 at 01:47:47 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3552 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5493149 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): -40.74300 16.01300 ymin,ymax (A): -12.02600 50.35400 zmin,zma (A): -51.52900 13.27900 x,y,z range (A): 56.75600 62.38000 64.80800 scale (grids/A): 0.5493149 object centre (A): -12.36500 19.16400 -19.12500 number of atom coordinates read : 3552 total number of charged atoms : 3408 net assigned charge : 11.95703 assigned positive charge : 531.0241 centred at (gu) : 89.76284 90.02209 91.81856 assigned negative charge : -519.0692 centred at (gu) : 89.88271 89.95547 92.02835 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7233 nv = 96 ne = 84 npr = 69321 no. pairs analyzed = 69321 no. exposed pairs = 4653 no. arc points = 34040 no. surface atoms = 1555 nbur = 1997 mkacc time = 0.1200000 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 = 1.540000 m= 287 mr = 3656 m= 0 mr = 14 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2500000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3465 ## 480 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7129052E-09 -1.6173299E-09 midg,1,midg; midg,igrid,midg 2.9333827E-10 1.4675520E-09 1,midg,midg; igrid,midg,midg 2.0290905E-09 -1.6894795E-10 gauss-seidel spectral radius is 0.9829688 estimated iterations to convergence 63 setup time was (sec) 0.4400000 now iterating at: 01:47:48 rms-change max change #iterations 8.4076963E-02 11.86704 at 10iterations 5.5309562E-03 0.9403965 at 20iterations 4.0103850E-04 5.8052063E-02 at 30iterations 3.3042896E-05 4.6358109E-03 at 40iterations 4.3623891E-06 4.4822693E-04 at 50iterations finished qdiffx linear iterations at : 01:47:50 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 4.3623891E-06 4.4822693E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 01:47:51 3.444u 0.175s 0:03.89 92.8% 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 01:47:51 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3552 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 1.647945 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): -40.74300 16.01300 ymin,ymax (A): -12.02600 50.35400 zmin,zma (A): -51.52900 13.27900 x,y,z range (A): 56.75600 62.38000 64.80800 scale (grids/A): 1.647945 object centre (A): -12.36500 19.16400 -19.12500 number of atom coordinates read : 3552 total number of charged atoms : 3408 net assigned charge : 11.95703 assigned positive charge : 531.0241 centred at (gu) : 89.28741 90.06512 95.45461 assigned negative charge : -519.0692 centred at (gu) : 89.64790 89.86617 96.08495 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34040 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24226 mr = 53351 m= 2496 mr = 16261 m= 80 mr = 1183 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1884 time to turn everything in is 0.3800000 number of dielectric boundary points 35892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 26174 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) : 0.5493149 object centre at (A) : -12.36500 19.16400 -19.12500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8779551E-02 4.7195205E-03 midg,1,midg; midg,igrid,midg 1.9123428E-02 3.1720124E-02 1,midg,midg; igrid,midg,midg 1.0177164E-02 -5.4646959E-03 gauss-seidel spectral radius is 0.9982936 estimated iterations to convergence 192 setup time was (sec) 0.6000000 now iterating at: 01:47:52 rms-change max change #iterations 3.741013 169.1099 at 10iterations 1.588296 61.96834 at 20iterations 0.6786005 23.70964 at 30iterations 0.2910666 9.562996 at 40iterations 0.1239208 3.992227 at 50iterations 5.3025536E-02 1.776217 at 60iterations 2.2659080E-02 0.8003497 at 70iterations 9.7326711E-03 0.3216829 at 80iterations 4.1604936E-03 0.1403003 at 90iterations 1.7831151E-03 5.8219910E-02 at 100iterations 7.6380512E-04 2.5884151E-02 at 110iterations 3.2694638E-04 1.2413025E-02 at 120iterations finished qdiffx linear iterations at : 01:47:59 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 3.2694638E-04 1.2413025E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 01:47:59 7.982u 0.214s 0:08.49 96.4% 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 01:47:59 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3552 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.471917 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): -40.74300 16.01300 ymin,ymax (A): -12.02600 50.35400 zmin,zma (A): -51.52900 13.27900 x,y,z range (A): 56.75600 62.38000 64.80800 scale (grids/A): 2.471917 object centre (A): -12.36500 19.16400 -19.12500 number of atom coordinates read : 3552 total number of charged atoms : 3408 net assigned charge : 11.95703 assigned positive charge : 531.0241 centred at (gu) : 88.93085 90.09747 98.18163 assigned negative charge : -519.0692 centred at (gu) : 89.47176 89.79925 99.12727 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 185650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34040 grid for indexing accessible points = 1.400000 m= 83700 mr = 130992 m= 23824 mr = 65199 m= 3880 mr = 17558 m= 263 mr = 2460 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 6556 time to turn everything in is 0.9500000 number of dielectric boundary points 80988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 27226 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) : 1.647945 object centre at (A) : -12.36500 19.16400 -19.12500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4565883 0.1274707 midg,1,midg; midg,igrid,midg 0.4484169 0.5338959 1,midg,midg; igrid,midg,midg 0.1507052 -3.7625652E-02 gauss-seidel spectral radius is 0.9991920 estimated iterations to convergence 278 setup time was (sec) 1.220000 now iterating at: 01:48:01 rms-change max change #iterations 9.752316 321.5536 at 10iterations 5.619814 157.9446 at 20iterations 3.221830 74.09019 at 30iterations 1.831622 41.68276 at 40iterations 1.040675 26.13664 at 50iterations 0.5884671 13.12910 at 60iterations 0.3320726 7.589993 at 70iterations 0.1867363 4.194717 at 80iterations 0.1049072 2.292118 at 90iterations 5.8987062E-02 1.146664 at 100iterations 3.3110537E-02 0.6813831 at 110iterations 1.8576067E-02 0.4056587 at 120iterations 1.0404704E-02 0.1827393 at 130iterations 5.8278986E-03 0.1138122 at 140iterations 3.2676675E-03 5.8908284E-02 at 150iterations 1.8279338E-03 3.4900665E-02 at 160iterations 1.0252834E-03 1.8518686E-02 at 170iterations 5.7567586E-04 1.0643005E-02 at 180iterations finished qdiffx linear iterations at : 01:48:13 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 5.7567586E-04 1.0643005E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 01:48:13 13.184u 0.249s 0:13.71 97.8% 0+0k 0+0io 0pf+0w