Sun Oct 9 23:04:30 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 Sun Oct 9 2011 at 23:04:30 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 = 4435 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5262147 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): -22.62200 31.47500 ymin,ymax (A): -86.49100 -18.83800 zmin,zma (A): -64.47600 -0.4080001 x,y,z range (A): 54.09700 67.65300 64.06800 scale (grids/A): 0.5262147 object centre (A): 4.426500 -52.66451 -32.44200 number of atom coordinates read : 4435 total number of charged atoms : 4273 net assigned charge : 4.000015 assigned positive charge : 671.3883 centred at (gu) : 89.72087 89.58518 91.67142 assigned negative charge : -667.3931 centred at (gu) : 89.81463 89.53825 91.79541 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8031 nv = 96 ne = 84 npr = 86363 no. pairs analyzed = 86363 no. exposed pairs = 5975 no. arc points = 41828 no. surface atoms = 2007 nbur = 2428 mkacc time = 0.1500000 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 = 1.652000 m= 327 mr = 4008 m= 0 mr = 8 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4192 ## 655 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4693230E-10 -7.1674194E-10 midg,1,midg; midg,igrid,midg -1.0725083E-10 3.0355460E-10 1,midg,midg; igrid,midg,midg 5.9081828E-10 -2.9332176E-10 gauss-seidel spectral radius is 0.9815157 estimated iterations to convergence 61 setup time was (sec) 0.4900000 now iterating at: 23:04:31 rms-change max change #iterations 7.3485509E-02 12.98725 at 10iterations 4.4868900E-03 0.6444550 at 20iterations 4.0291453E-04 8.3594322E-02 at 30iterations 1.0139877E-04 2.3457527E-02 at 40iterations 3.3860455E-05 7.7705383E-03 at 50iterations finished qdiffx linear iterations at : 23:04:34 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 3.3860455E-05 7.7705383E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 23:04:34 3.520u 0.169s 0:04.04 91.0% 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 Sun Oct 9 2011 at 23:04:34 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 = 4435 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.578644 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): -22.62200 31.47500 ymin,ymax (A): -86.49100 -18.83800 zmin,zma (A): -64.47600 -0.4080001 x,y,z range (A): 54.09700 67.65300 64.06800 scale (grids/A): 1.578644 object centre (A): 4.426500 -52.66451 -32.44200 number of atom coordinates read : 4435 total number of charged atoms : 4273 net assigned charge : 4.000015 assigned positive charge : 671.3883 centred at (gu) : 89.16080 88.75413 95.01223 assigned negative charge : -667.3931 centred at (gu) : 89.44312 88.61427 95.38587 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41828 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25823 mr = 59691 m= 2394 mr = 17018 m= 43 mr = 1019 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 40440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 568 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 32434 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) : 0.5262147 object centre at (A) : 4.426500 -52.66451 -32.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9804277E-02 1.0614882E-02 midg,1,midg; midg,igrid,midg -3.4251760E-04 1.0343477E-02 1,midg,midg; igrid,midg,midg -4.1945459E-04 -1.3939179E-02 gauss-seidel spectral radius is 0.9982240 estimated iterations to convergence 188 setup time was (sec) 0.6700000 now iterating at: 23:04:35 rms-change max change #iterations 3.855698 159.1927 at 10iterations 1.608608 60.01706 at 20iterations 0.6743219 29.95717 at 30iterations 0.2839694 8.558838 at 40iterations 0.1195531 3.794205 at 50iterations 5.0203737E-02 1.653614 at 60iterations 2.1087032E-02 0.7453737 at 70iterations 8.8847112E-03 0.2970247 at 80iterations 3.7503885E-03 0.1283398 at 90iterations 1.5971920E-03 5.2730322E-02 at 100iterations 6.8671763E-04 2.0618439E-02 at 110iterations 3.0589470E-04 9.7141266E-03 at 120iterations finished qdiffx linear iterations at : 23:04:42 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.0589470E-04 9.7141266E-03 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 23:04:43 7.948u 0.194s 0:08.52 95.4% 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 23:04:43 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 = 4435 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.367966 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): -22.62200 31.47500 ymin,ymax (A): -86.49100 -18.83800 zmin,zma (A): -64.47600 -0.4080001 x,y,z range (A): 54.09700 67.65300 64.06800 scale (grids/A): 2.367966 object centre (A): 4.426500 -52.66451 -32.44200 number of atom coordinates read : 4435 total number of charged atoms : 4273 net assigned charge : 4.000015 assigned positive charge : 671.3883 centred at (gu) : 88.74066 88.13065 97.51790 assigned negative charge : -667.3931 centred at (gu) : 89.16457 87.92143 98.07857 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 209189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41828 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 92260 mr = 147077 m= 23344 mr = 71330 m= 3417 mr = 16587 m= 214 mr = 2078 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 91298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 34123 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) : 1.578644 object centre at (A) : 4.426500 -52.66451 -32.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3002107 0.3337961 midg,1,midg; midg,igrid,midg 1.4259272E-02 0.3075088 1,midg,midg; igrid,midg,midg -1.5705081E-02 -0.1891208 gauss-seidel spectral radius is 0.9991957 estimated iterations to convergence 278 setup time was (sec) 1.290000 now iterating at: 23:04:44 rms-change max change #iterations 10.43014 286.2292 at 10iterations 6.118386 164.2541 at 20iterations 3.544684 74.88528 at 30iterations 2.035270 52.08630 at 40iterations 1.166087 29.30963 at 50iterations 0.6638243 12.80877 at 60iterations 0.3766119 7.532780 at 70iterations 0.2133048 3.966778 at 80iterations 0.1205760 2.216008 at 90iterations 6.8172969E-02 1.526802 at 100iterations 3.8412504E-02 0.7503738 at 110iterations 2.1655437E-02 0.3895454 at 120iterations 1.2187609E-02 0.2041702 at 130iterations 6.8476833E-03 0.1241512 at 140iterations 3.8593330E-03 6.8370819E-02 at 150iterations 2.1707809E-03 3.8848877E-02 at 160iterations 1.2263012E-03 2.1544456E-02 at 170iterations 6.9322024E-04 1.1834502E-02 at 180iterations finished qdiffx linear iterations at : 23:04:56 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 6.9322024E-04 1.1834502E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 23:04:56 13.059u 0.228s 0:13.67 97.0% 0+0k 0+0io 0pf+0w