Mon Oct 10 17:09:03 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 Mon Oct 10 2011 at 17:09:03 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 = 2774 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5821273 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): 1.791000 62.94600 ymin,ymax (A): 11.97400 63.11200 zmin,zma (A): -7.338000 41.99000 x,y,z range (A): 61.15500 51.13800 49.32800 scale (grids/A): 0.5821273 object centre (A): 32.36850 37.54300 17.32600 number of atom coordinates read : 2774 total number of charged atoms : 2635 net assigned charge : -1.499975 assigned positive charge : 414.9332 centred at (gu) : 89.83080 88.87870 89.01575 assigned negative charge : -416.4343 centred at (gu) : 89.90477 89.13274 88.86135 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6231 nv = 96 ne = 84 npr = 54367 no. pairs analyzed = 54367 no. exposed pairs = 3736 no. arc points = 26464 no. surface atoms = 1258 nbur = 1516 mkacc time = 9.9999994E-02 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 = 1.484000 m= 278 mr = 3102 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2610 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7859 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8680202E-09 2.3524764E-09 midg,1,midg; midg,igrid,midg 6.6314754E-09 -4.7296660E-09 1,midg,midg; igrid,midg,midg 1.2943435E-09 -1.9458408E-09 gauss-seidel spectral radius is 0.9847587 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 17:09:03 rms-change max change #iterations 9.6020550E-02 15.50834 at 10iterations 7.3955581E-03 1.263652 at 20iterations 5.9971481E-04 8.1867218E-02 at 30iterations 5.2449959E-05 9.9239349E-03 at 40iterations 6.5690838E-06 1.1503696E-03 at 50iterations finished qdiffx linear iterations at : 17:09:06 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 6.5690838E-06 1.1503696E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 17:09:07 3.357u 0.165s 0:04.36 80.5% 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 Mon Oct 10 2011 at 17:09:07 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 = 2774 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.746382 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): 1.791000 62.94600 ymin,ymax (A): 11.97400 63.11200 zmin,zma (A): -7.338000 41.99000 x,y,z range (A): 61.15500 51.13800 49.32800 scale (grids/A): 1.746382 object centre (A): 32.36850 37.54300 17.32600 number of atom coordinates read : 2774 total number of charged atoms : 2635 net assigned charge : -1.499975 assigned positive charge : 414.9332 centred at (gu) : 89.49177 86.63515 87.04636 assigned negative charge : -416.4343 centred at (gu) : 89.71391 87.39764 86.58379 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26464 grid for indexing accessible points = 1.400000 m= 21306 mr = 45583 m= 2453 mr = 14375 m= 96 mr = 1199 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 31356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20474 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) : 0.5821273 object centre at (A) : 32.36850 37.54300 17.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7098368E-03 2.2617485E-03 midg,1,midg; midg,igrid,midg 2.0726621E-02 -2.2559496E-02 1,midg,midg; igrid,midg,midg 1.2563102E-02 -4.0861508E-03 gauss-seidel spectral radius is 0.9984100 estimated iterations to convergence 199 setup time was (sec) 0.5300000 now iterating at: 17:09:08 rms-change max change #iterations 3.686082 167.9929 at 10iterations 1.618670 67.29369 at 20iterations 0.7113391 24.67272 at 30iterations 0.3131888 10.98558 at 40iterations 0.1380037 4.727339 at 50iterations 6.0926903E-02 2.044462 at 60iterations 2.6822496E-02 0.8993568 at 70iterations 1.1844848E-02 0.4211230 at 80iterations 5.2247564E-03 0.1975508 at 90iterations 2.3119410E-03 7.8987122E-02 at 100iterations 1.0169448E-03 3.5696030E-02 at 110iterations 4.4760419E-04 1.6144514E-02 at 120iterations finished qdiffx linear iterations at : 17:09:15 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 4.4760419E-04 1.6144514E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 17:09:16 7.600u 0.216s 0:09.06 86.2% 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 Mon Oct 10 2011 at 17:09:17 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 = 2774 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.619573 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): 1.791000 62.94600 ymin,ymax (A): 11.97400 63.11200 zmin,zma (A): -7.338000 41.99000 x,y,z range (A): 61.15500 51.13800 49.32800 scale (grids/A): 2.619573 object centre (A): 32.36850 37.54300 17.32600 number of atom coordinates read : 2774 total number of charged atoms : 2635 net assigned charge : -1.499975 assigned positive charge : 414.9332 centred at (gu) : 89.23765 84.95243 85.56952 assigned negative charge : -416.4343 centred at (gu) : 89.57080 86.09637 84.87559 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 159208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26464 grid for indexing accessible points = 1.400000 m= 72010 mr = 111381 m= 21654 mr = 56138 m= 3934 mr = 16093 m= 335 mr = 2602 m= 6 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 70764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21076 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) : 1.746382 object centre at (A) : 32.36850 37.54300 17.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6428853E-02 1.2261822E-02 midg,1,midg; midg,igrid,midg 0.2753622 -0.2714666 1,midg,midg; igrid,midg,midg 0.1806537 6.4017437E-02 gauss-seidel spectral radius is 0.9992096 estimated iterations to convergence 281 setup time was (sec) 1.040000 now iterating at: 17:09:18 rms-change max change #iterations 9.239475 366.6778 at 10iterations 5.324072 141.9503 at 20iterations 3.061146 82.72908 at 30iterations 1.747736 38.82361 at 40iterations 0.9936666 25.46831 at 50iterations 0.5656908 13.32319 at 60iterations 0.3215885 7.234327 at 70iterations 0.1821438 3.768066 at 80iterations 0.1031578 2.423471 at 90iterations 5.8134343E-02 1.228639 at 100iterations 3.2936633E-02 0.7439671 at 110iterations 1.8585289E-02 0.3765440 at 120iterations 1.0503056E-02 0.2180979 at 130iterations 5.9256507E-03 0.1173649 at 140iterations 3.3411626E-03 6.9387913E-02 at 150iterations 1.8851102E-03 3.7699223E-02 at 160iterations 1.0632966E-03 2.1636963E-02 at 170iterations 6.0039858E-04 1.2312889E-02 at 180iterations finished qdiffx linear iterations at : 17:09:29 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 6.0039858E-04 1.2312889E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 17:09:29 12.145u 0.216s 0:12.69 97.3% 0+0k 0+0io 0pf+0w