Sat Oct 15 14:48:59 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 Sat Oct 15 2011 at 14:48:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 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: 0.5741751 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): 2.351000 64.35300 ymin,ymax (A): -24.57000 24.42100 zmin,zma (A): 2.049000 49.31700 x,y,z range (A): 62.00200 48.99100 47.26800 scale (grids/A): 0.5741751 object centre (A): 33.35200 -7.4500084E-02 25.68300 number of atom coordinates read : 2861 total number of charged atoms : 2720 net assigned charge : -1.999972 assigned positive charge : 427.7831 centred at (gu) : 89.28439 90.04987 90.30817 assigned negative charge : -429.7842 centred at (gu) : 89.32139 89.90231 90.47567 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6254 nv = 96 ne = 84 npr = 57069 no. pairs analyzed = 57069 no. exposed pairs = 3786 no. arc points = 26869 no. surface atoms = 1267 nbur = 1594 mkacc time = 0.1600000 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 = 1.512000 m= 304 mr = 3185 m= 4 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3300000 number of dielectric boundary points 3361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2713 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7969 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3462698E-09 -3.5980980E-09 midg,1,midg; midg,igrid,midg -2.9433280E-09 2.2179343E-09 1,midg,midg; igrid,midg,midg 3.5693207E-10 -8.4378199E-10 gauss-seidel spectral radius is 0.9843436 estimated iterations to convergence 66 setup time was (sec) 0.6800000 now iterating at: 14:49:00 rms-change max change #iterations 9.1294728E-02 15.33310 at 10iterations 6.9124526E-03 0.9982491 at 20iterations 5.3237716E-04 8.2214355E-02 at 30iterations 4.0513492E-05 5.8593750E-03 at 40iterations 3.1547388E-06 4.8446655E-04 at 50iterations finished qdiffx linear iterations at : 14:49:04 total time elapsed so far: 5.120000 # loops : 50 mean,max change (kT/e) : 3.1547388E-06 4.8446655E-04 energy calculations done at 5.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 14:49:05 5.294u 0.424s 0:06.06 94.2% 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 Sat Oct 15 2011 at 14:49:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 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: 1.722525 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): 2.351000 64.35300 ymin,ymax (A): -24.57000 24.42100 zmin,zma (A): 2.049000 49.31700 x,y,z range (A): 62.00200 48.99100 47.26800 scale (grids/A): 1.722525 object centre (A): 33.35200 -7.4500084E-02 25.68300 number of atom coordinates read : 2861 total number of charged atoms : 2720 net assigned charge : -1.999972 assigned positive charge : 427.7831 centred at (gu) : 87.85230 90.14927 90.92371 assigned negative charge : -429.7842 centred at (gu) : 87.96372 89.70675 91.42660 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26869 grid for indexing accessible points = 1.400000 m= 21913 mr = 45862 m= 2670 mr = 15082 m= 104 mr = 1415 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1552 time to turn everything in is 0.6000000 number of dielectric boundary points 31121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21116 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) : 0.5741751 object centre at (A) : 33.35200 -7.4500084E-02 25.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0264146E-03 -7.7796034E-03 midg,1,midg; midg,igrid,midg -2.2397157E-02 1.2222223E-02 1,midg,midg; igrid,midg,midg -1.3072579E-03 -3.9232571E-02 gauss-seidel spectral radius is 0.9983705 estimated iterations to convergence 197 setup time was (sec) 0.9900000 now iterating at: 14:49:06 rms-change max change #iterations 3.641803 160.2753 at 10iterations 1.578215 57.43297 at 20iterations 0.6879310 25.02239 at 30iterations 0.2995788 11.05562 at 40iterations 0.1308416 4.952397 at 50iterations 5.6837521E-02 2.149365 at 60iterations 2.4751602E-02 0.9264488 at 70iterations 1.0817914E-02 0.3957500 at 80iterations 4.7485121E-03 0.1676626 at 90iterations 2.0578955E-03 7.5298309E-02 at 100iterations 8.9940289E-04 3.1404197E-02 at 110iterations 3.9300401E-04 1.3805389E-02 at 120iterations finished qdiffx linear iterations at : 14:49:18 total time elapsed so far: 12.98000 # loops : 120 mean,max change (kT/e) : 3.9300401E-04 1.3805389E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 14:49:19 13.164u 0.479s 0:14.00 97.3% 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 Sat Oct 15 2011 at 14:49:19 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 = 2861 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: 2.583788 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): 2.351000 64.35300 ymin,ymax (A): -24.57000 24.42100 zmin,zma (A): 2.049000 49.31700 x,y,z range (A): 62.00200 48.99100 47.26800 scale (grids/A): 2.583788 object centre (A): 33.35200 -7.4500084E-02 25.68300 number of atom coordinates read : 2861 total number of charged atoms : 2720 net assigned charge : -1.999972 assigned positive charge : 427.7831 centred at (gu) : 86.77827 90.22340 91.38528 assigned negative charge : -429.7842 centred at (gu) : 86.94555 89.56003 92.13982 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 159892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26869 grid for indexing accessible points = 1.400000 m= 74092 mr = 112426 m= 22915 mr = 58445 m= 4331 mr = 17323 m= 460 mr = 2978 m= 19 mr = 276 m= 0 mr = 13 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 4946 time to turn everything in is 1.530000 number of dielectric boundary points 70248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 21750 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) : 1.722525 object centre at (A) : 33.35200 -7.4500084E-02 25.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6813375E-02 -8.8240236E-02 midg,1,midg; midg,igrid,midg -0.2617631 0.1866401 1,midg,midg; igrid,midg,midg 5.2747261E-02 -0.7517301 gauss-seidel spectral radius is 0.9991981 estimated iterations to convergence 279 setup time was (sec) 1.970000 now iterating at: 14:49:21 rms-change max change #iterations 9.182530 278.2329 at 10iterations 5.267883 142.6226 at 20iterations 2.993835 74.23412 at 30iterations 1.699495 42.67945 at 40iterations 0.9627686 19.41912 at 50iterations 0.5440752 11.76099 at 60iterations 0.3067107 6.418442 at 70iterations 0.1729240 3.570305 at 80iterations 9.7361356E-02 2.032982 at 90iterations 5.4720625E-02 1.209244 at 100iterations 3.0754209E-02 0.6744957 at 110iterations 1.7282197E-02 0.3883305 at 120iterations 9.7273402E-03 0.1847286 at 130iterations 5.4648654E-03 0.1084185 at 140iterations 3.0684182E-03 5.6263924E-02 at 150iterations 1.7274154E-03 3.4182549E-02 at 160iterations 9.7694714E-04 1.9510508E-02 at 170iterations 5.5204070E-04 1.1810303E-02 at 180iterations finished qdiffx linear iterations at : 14:49:41 total time elapsed so far: 21.84000 # loops : 180 mean,max change (kT/e) : 5.5204070E-04 1.1810303E-02 energy calculations done at 21.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.01000 DelPhi exited at 14:49:42 22.017u 0.520s 0:22.97 98.0% 0+0k 0+0io 0pf+0w