Sun Oct 9 21:17:45 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 21:17:45 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 = 3026 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: 0.5880604 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): 2.057000 58.13300 ymin,ymax (A): 23.95500 84.49300 zmin,zma (A): -23.51700 28.94500 x,y,z range (A): 56.07600 60.53799 52.46200 scale (grids/A): 0.5880604 object centre (A): 30.09500 54.22400 2.714000 number of atom coordinates read : 3026 total number of charged atoms : 2977 net assigned charge : 4.500015 assigned positive charge : 473.2658 centred at (gu) : 88.66972 88.94361 90.55506 assigned negative charge : -468.7672 centred at (gu) : 88.62437 88.80178 90.55724 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7084 nv = 96 ne = 84 npr = 56435 no. pairs analyzed = 56435 no. exposed pairs = 4112 no. arc points = 30181 no. surface atoms = 1359 nbur = 1667 mkacc time = 0.1400000 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 = 1.456000 m= 315 mr = 3505 m= 0 mr = 35 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3124 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2651944E-09 1.4746254E-09 midg,1,midg; midg,igrid,midg -3.8423345E-09 4.3603556E-09 1,midg,midg; igrid,midg,midg -3.4801970E-11 2.0119226E-09 gauss-seidel spectral radius is 0.9850875 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 21:17:46 rms-change max change #iterations 0.1090433 17.20070 at 10iterations 8.4898099E-03 1.188616 at 20iterations 6.8716600E-04 0.1177549 at 30iterations 5.7401994E-05 9.0875626E-03 at 40iterations 6.0553139E-06 8.7738037E-04 at 50iterations finished qdiffx linear iterations at : 21:17:48 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.0553139E-06 8.7738037E-04 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 21:17:49 3.361u 0.149s 0:03.81 91.8% 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 21:17:49 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 = 3026 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: 1.764181 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): 2.057000 58.13300 ymin,ymax (A): 23.95500 84.49300 zmin,zma (A): -23.51700 28.94500 x,y,z range (A): 56.07600 60.53799 52.46200 scale (grids/A): 1.764181 object centre (A): 30.09500 54.22400 2.714000 number of atom coordinates read : 3026 total number of charged atoms : 2977 net assigned charge : 4.500015 assigned positive charge : 473.2658 centred at (gu) : 86.00859 86.83014 91.66476 assigned negative charge : -468.7672 centred at (gu) : 85.87267 86.40508 91.67178 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 grid for indexing accessible points = 1.400000 m= 24637 mr = 50721 m= 3219 mr = 16849 m= 133 mr = 1815 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 710 time to turn everything in is 0.5700000 number of dielectric boundary points 35783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23112 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) : 0.5880604 object centre at (A) : 30.09500 54.22400 2.714000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4230519E-03 -1.8264806E-03 midg,1,midg; midg,igrid,midg -3.6945019E-03 2.0352857E-02 1,midg,midg; igrid,midg,midg 4.9685766E-03 -9.1172084E-03 gauss-seidel spectral radius is 0.9984782 estimated iterations to convergence 203 setup time was (sec) 0.8500000 now iterating at: 21:17:50 rms-change max change #iterations 4.029113 160.2936 at 10iterations 1.790525 67.33438 at 20iterations 0.8011971 27.98306 at 30iterations 0.3598014 11.46561 at 40iterations 0.1610822 5.824532 at 50iterations 7.2068885E-02 2.405354 at 60iterations 3.2271437E-02 1.046247 at 70iterations 1.4417705E-02 0.4592590 at 80iterations 6.4853821E-03 0.1994400 at 90iterations 2.9072016E-03 9.4011307E-02 at 100iterations 1.3036032E-03 4.0054321E-02 at 110iterations 5.8791757E-04 1.9012451E-02 at 120iterations finished qdiffx linear iterations at : 21:17:56 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 5.8791757E-04 1.9012451E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 21:17:57 7.447u 0.160s 0:07.98 95.2% 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 21:17:57 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 = 3026 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: 2.646272 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): 2.057000 58.13300 ymin,ymax (A): 23.95500 84.49300 zmin,zma (A): -23.51700 28.94500 x,y,z range (A): 56.07600 60.53799 52.46200 scale (grids/A): 2.646272 object centre (A): 30.09500 54.22400 2.714000 number of atom coordinates read : 3026 total number of charged atoms : 2977 net assigned charge : 4.500015 assigned positive charge : 473.2658 centred at (gu) : 84.01267 85.24487 92.49696 assigned negative charge : -468.7672 centred at (gu) : 83.80894 84.60763 92.50735 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 178690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 grid for indexing accessible points = 1.400000 m= 82922 mr = 124108 m= 26068 mr = 65015 m= 5422 mr = 19692 m= 630 mr = 3907 m= 17 mr = 387 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 2633 time to turn everything in is 1.380000 number of dielectric boundary points 80640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 23805 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) : 1.764181 object centre at (A) : 30.09500 54.22400 2.714000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9186839E-02 -7.4778214E-02 midg,1,midg; midg,igrid,midg -0.1744052 0.2631246 1,midg,midg; igrid,midg,midg -8.2449719E-02 -0.1988872 gauss-seidel spectral radius is 0.9992423 estimated iterations to convergence 287 setup time was (sec) 1.680000 now iterating at: 21:17:59 rms-change max change #iterations 10.06745 344.7728 at 10iterations 5.930694 162.0919 at 20iterations 3.462593 82.79375 at 30iterations 2.016796 56.16322 at 40iterations 1.166965 24.36316 at 50iterations 0.6743218 16.27111 at 60iterations 0.3886846 9.239988 at 70iterations 0.2230538 4.756244 at 80iterations 0.1279495 2.726552 at 90iterations 7.3356256E-02 1.477188 at 100iterations 4.2064939E-02 0.8598175 at 110iterations 2.4107059E-02 0.4772873 at 120iterations 1.3765118E-02 0.2663932 at 130iterations 7.8727994E-03 0.1526120 at 140iterations 4.5098029E-03 8.4505081E-02 at 150iterations 2.5708952E-03 5.2593231E-02 at 160iterations 1.4689640E-03 2.8347015E-02 at 170iterations 8.4012782E-04 1.7903805E-02 at 180iterations finished qdiffx linear iterations at : 21:18:09 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 8.4012782E-04 1.7903805E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 21:18:10 12.004u 0.174s 0:12.60 96.5% 0+0k 0+0io 0pf+0w