Sat Oct 15 13:44:11 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 Sat Oct 15 2011 at 13:44:11 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4072 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: 0.5589663 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): 13.10600 73.70600 ymin,ymax (A): 128.8950 192.5840 zmin,zma (A): -7.094000 52.95200 x,y,z range (A): 60.60000 63.68900 60.04600 scale (grids/A): 0.5589663 object centre (A): 43.40600 160.7395 22.92900 number of atom coordinates read : 4072 total number of charged atoms : 3487 net assigned charge : 18.00000 assigned positive charge : 542.8445 centred at (gu) : 89.29012 89.69855 91.31669 assigned negative charge : -524.8460 centred at (gu) : 89.29467 89.86131 91.44475 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8434 nv = 96 ne = 84 npr = 81370 no. pairs analyzed = 81370 no. exposed pairs = 5884 no. arc points = 41102 no. surface atoms = 1950 nbur = 2122 mkacc time = 0.2100000 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 = 1.568000 m= 401 mr = 4012 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3483 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9655 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5154934E-09 2.6608807E-10 midg,1,midg; midg,igrid,midg 4.1550146E-09 -2.0866235E-10 1,midg,midg; igrid,midg,midg 2.2638076E-09 1.5249326E-09 gauss-seidel spectral radius is 0.9835934 estimated iterations to convergence 64 setup time was (sec) 0.7700000 now iterating at: 13:44:12 rms-change max change #iterations 9.3131885E-02 16.60670 at 10iterations 6.9313361E-03 1.026801 at 20iterations 9.0959133E-04 0.1326065 at 30iterations 3.0035916E-04 3.7926674E-02 at 40iterations 1.1403846E-04 1.4507294E-02 at 50iterations finished qdiffx linear iterations at : 13:44:17 total time elapsed so far: 5.450000 # loops : 50 mean,max change (kT/e) : 1.1403846E-04 1.4507294E-02 energy calculations done at 5.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.610000 DelPhi exited at 13:44:18 5.617u 0.507s 0:06.93 88.1% 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 Sat Oct 15 2011 at 13:44:18 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.676899 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): 13.10600 73.70600 ymin,ymax (A): 128.8950 192.5840 zmin,zma (A): -7.094000 52.95200 x,y,z range (A): 60.60000 63.68900 60.04600 scale (grids/A): 1.676899 object centre (A): 43.40600 160.7395 22.92900 number of atom coordinates read : 4072 total number of charged atoms : 3487 net assigned charge : 18.00000 assigned positive charge : 542.8445 centred at (gu) : 87.86969 89.09476 93.94965 assigned negative charge : -524.8460 centred at (gu) : 87.88344 89.58365 94.33372 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 91725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41102 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29332 mr = 59156 m= 3506 mr = 19220 m= 108 mr = 1739 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 44543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 368 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 26799 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) : 0.5589663 object centre at (A) : 43.40600 160.7395 22.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7662236E-02 1.6818939E-02 midg,1,midg; midg,igrid,midg 5.1872019E-02 -9.4862180E-03 1,midg,midg; igrid,midg,midg 2.7314348E-02 2.0366810E-02 gauss-seidel spectral radius is 0.9984191 estimated iterations to convergence 200 setup time was (sec) 1.160000 now iterating at: 13:44:20 rms-change max change #iterations 3.959474 163.3729 at 10iterations 1.744956 65.26723 at 20iterations 0.7734556 29.27087 at 30iterations 0.3394603 12.56052 at 40iterations 0.1504493 4.609070 at 50iterations 6.6407993E-02 2.045052 at 60iterations 2.9427154E-02 0.9269321 at 70iterations 1.3029600E-02 0.3783360 at 80iterations 5.7821623E-03 0.1696606 at 90iterations 2.6020433E-03 8.1588745E-02 at 100iterations 1.1931794E-03 4.0975735E-02 at 110iterations 5.7890627E-04 1.7642021E-02 at 120iterations finished qdiffx linear iterations at : 13:44:35 total time elapsed so far: 13.61000 # loops : 120 mean,max change (kT/e) : 5.7890627E-04 1.7642021E-02 energy calculations done at 13.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 13:44:35 13.785u 0.572s 0:17.20 83.4% 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 Sat Oct 15 2011 at 13:44:35 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4072 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: 2.515348 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): 13.10600 73.70600 ymin,ymax (A): 128.8950 192.5840 zmin,zma (A): -7.094000 52.95200 x,y,z range (A): 60.60000 63.68900 60.04600 scale (grids/A): 2.515348 object centre (A): 43.40600 160.7395 22.92900 number of atom coordinates read : 4072 total number of charged atoms : 3487 net assigned charge : 18.00000 assigned positive charge : 542.8445 centred at (gu) : 86.80403 88.64172 95.92428 assigned negative charge : -524.8460 centred at (gu) : 86.82518 89.37556 96.50053 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 212453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41102 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 97964 mr = 145540 m= 30218 mr = 74573 m= 5628 mr = 22141 m= 483 mr = 3745 m= 11 mr = 211 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 100548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 27877 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) : 1.676899 object centre at (A) : 43.40600 160.7395 22.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3514894 0.3141420 midg,1,midg; midg,igrid,midg 0.6588613 -0.1865994 1,midg,midg; igrid,midg,midg 0.2252123 0.2149334 gauss-seidel spectral radius is 0.9992540 estimated iterations to convergence 289 setup time was (sec) 2.470000 now iterating at: 13:44:39 rms-change max change #iterations 10.29083 332.3710 at 10iterations 6.117079 150.6222 at 20iterations 3.604194 77.44881 at 30iterations 2.111579 45.57698 at 40iterations 1.232231 24.66208 at 50iterations 0.7168806 14.15936 at 60iterations 0.4156216 8.922415 at 70iterations 0.2408202 4.345559 at 80iterations 0.1388895 2.794666 at 90iterations 8.0172613E-02 1.380186 at 100iterations 4.6327531E-02 0.8558855 at 110iterations 2.6628200E-02 0.5264578 at 120iterations 1.5346052E-02 0.2991180 at 130iterations 8.8096131E-03 0.1567078 at 140iterations 5.0684824E-03 8.8749886E-02 at 150iterations 2.9093085E-03 5.6854248E-02 at 160iterations 1.6727812E-03 2.9792428E-02 at 170iterations 9.6068758E-04 1.7127991E-02 at 180iterations finished qdiffx linear iterations at : 13:45:00 total time elapsed so far: 23.26000 # loops : 180 mean,max change (kT/e) : 9.6068758E-04 1.7127991E-02 energy calculations done at 23.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.42000 DelPhi exited at 13:45:00 23.423u 0.604s 0:24.89 96.5% 0+0k 0+0io 0pf+0w