Tue Oct 11 06:02:46 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 Tue Oct 11 2011 at 06:02:46 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7032099 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): 25.73400 72.08400 ymin,ymax (A): -18.99700 31.62800 zmin,zma (A): 3.910000 46.22100 x,y,z range (A): 46.35000 50.62500 42.31100 scale (grids/A): 0.7032099 object centre (A): 48.90900 6.315500 25.06550 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 89.24531 90.24355 90.39308 assigned negative charge : -320.8621 centred at (gu) : 89.36790 90.17973 90.47977 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7149 nv = 96 ne = 84 npr = 42736 no. pairs analyzed = 42736 no. exposed pairs = 2603 no. arc points = 17594 no. surface atoms = 889 nbur = 1438 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4082 m= 2 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1602 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7914 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5838486E-08 1.6023625E-09 midg,1,midg; midg,igrid,midg 1.1941986E-08 7.4893798E-08 1,midg,midg; igrid,midg,midg 1.1380028E-07 -1.2805251E-08 gauss-seidel spectral radius is 0.9894634 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 06:02:47 rms-change max change #iterations 0.1980719 33.59978 at 10iterations 2.5169602E-02 3.696388 at 20iterations 3.8346045E-03 0.5007401 at 30iterations 8.5884705E-04 0.1011353 at 40iterations 2.6331050E-04 2.9792786E-02 at 50iterations finished qdiffx linear iterations at : 06:02:50 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.6331050E-04 2.9792786E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 06:02:51 3.390u 0.168s 0:04.92 72.1% 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 Tue Oct 11 2011 at 06:02:51 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.109630 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): 25.73400 72.08400 ymin,ymax (A): -18.99700 31.62800 zmin,zma (A): 3.910000 46.22100 x,y,z range (A): 46.35000 50.62500 42.31100 scale (grids/A): 2.109630 object centre (A): 48.90900 6.315500 25.06550 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 87.73591 90.73067 91.17938 assigned negative charge : -320.8621 centred at (gu) : 88.10378 90.53924 91.43945 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17594 grid for indexing accessible points = 1.400000 m= 30745 mr = 53839 m= 5949 mr = 23288 m= 560 mr = 4037 m= 20 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15842 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) : 0.7032099 object centre at (A) : 48.90900 6.315500 25.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8773673E-02 2.3637492E-02 midg,1,midg; midg,igrid,midg 3.9673019E-02 2.8104495E-02 1,midg,midg; igrid,midg,midg 3.9296959E-02 -4.4787552E-02 gauss-seidel spectral radius is 0.9988223 estimated iterations to convergence 231 setup time was (sec) 0.6000000 now iterating at: 06:02:52 rms-change max change #iterations 4.642453 183.6506 at 10iterations 2.290577 81.33650 at 20iterations 1.132231 34.10958 at 30iterations 0.5623852 18.89969 at 40iterations 0.2789945 8.832981 at 50iterations 0.1383476 4.393463 at 60iterations 6.8629704E-02 1.977095 at 70iterations 3.4158278E-02 0.9965023 at 80iterations 1.7219927E-02 0.5040989 at 90iterations 8.6854845E-03 0.2680168 at 100iterations 4.4828728E-03 0.1338654 at 110iterations 2.4169197E-03 7.5281143E-02 at 120iterations finished qdiffx linear iterations at : 06:02:59 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.4169197E-03 7.5281143E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 06:03:00 7.872u 0.207s 0:09.04 89.2% 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 Tue Oct 11 2011 at 06:03:00 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.164444 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): 25.73400 72.08400 ymin,ymax (A): -18.99700 31.62800 zmin,zma (A): 3.910000 46.22100 x,y,z range (A): 46.35000 50.62500 42.31100 scale (grids/A): 3.164444 object centre (A): 48.90900 6.315500 25.06550 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 86.60373 91.09613 91.76905 assigned negative charge : -320.8621 centred at (gu) : 87.15568 90.80876 92.15911 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17594 grid for indexing accessible points = 1.400000 m= 95349 mr = 129455 m= 39075 mr = 79363 m= 11186 mr = 32131 m= 2235 mr = 8756 m= 290 mr = 1589 m= 16 mr = 183 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15984 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) : 2.109630 object centre at (A) : 48.90900 6.315500 25.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1045963 0.2082353 midg,1,midg; midg,igrid,midg 0.2859170 0.1241968 1,midg,midg; igrid,midg,midg 0.4042982 -0.5506631 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 06:03:02 rms-change max change #iterations 10.42007 469.0214 at 10iterations 6.185019 142.5206 at 20iterations 3.658057 72.66991 at 30iterations 2.160510 42.76601 at 40iterations 1.273833 25.93651 at 50iterations 0.7500463 13.63616 at 60iterations 0.4407722 7.689095 at 70iterations 0.2582521 4.619686 at 80iterations 0.1517236 2.624069 at 90iterations 8.9047208E-02 1.606522 at 100iterations 5.2480567E-02 0.9303360 at 110iterations 3.0951111E-02 0.5638733 at 120iterations 1.8412445E-02 0.3407717 at 130iterations 1.1144670E-02 0.2028847 at 140iterations 6.9176615E-03 0.1398659 at 150iterations 4.4499221E-03 8.9458466E-02 at 160iterations 3.0376359E-03 5.6358337E-02 at 170iterations 2.2015406E-03 4.4456482E-02 at 180iterations finished qdiffx linear iterations at : 06:03:13 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 2.2015406E-03 4.4456482E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 06:03:14 13.224u 0.227s 0:13.93 96.4% 0+0k 0+0io 0pf+0w