Mon Oct 10 19:34:24 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 19:34:24 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6389318 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): -12.10600 40.68000 ymin,ymax (A): -28.45500 23.72300 zmin,zma (A): -9.321000 46.39700 x,y,z range (A): 52.78600 52.17800 55.71800 scale (grids/A): 0.6389318 object centre (A): 14.28700 -2.366000 18.53800 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : -1.999976 assigned positive charge : 407.5195 centred at (gu) : 89.99318 89.28333 90.60271 assigned negative charge : -409.5207 centred at (gu) : 90.02110 89.24777 90.71227 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7599 nv = 96 ne = 84 npr = 55347 no. pairs analyzed = 55347 no. exposed pairs = 3723 no. arc points = 25969 no. surface atoms = 1233 nbur = 1501 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3906 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3300000 number of dielectric boundary points 4090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2499 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9007 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9653174E-09 -1.8172202E-08 midg,1,midg; midg,igrid,midg -8.1152471E-09 1.2976344E-09 1,midg,midg; igrid,midg,midg 6.3550343E-10 -6.0297034E-09 gauss-seidel spectral radius is 0.9873304 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 19:34:25 rms-change max change #iterations 0.1495807 23.57567 at 10iterations 1.4758428E-02 2.104651 at 20iterations 1.5401024E-03 0.2252274 at 30iterations 2.1391925E-04 3.7284851E-02 at 40iterations 4.9010407E-05 9.5977783E-03 at 50iterations finished qdiffx linear iterations at : 19:34:30 total time elapsed so far: 5.280000 # loops : 50 mean,max change (kT/e) : 4.9010407E-05 9.5977783E-03 energy calculations done at 5.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.450000 DelPhi exited at 19:34:31 5.450u 0.420s 0:06.28 93.4% 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 Mon Oct 10 2011 at 19:34:31 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.916795 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): -12.10600 40.68000 ymin,ymax (A): -28.45500 23.72300 zmin,zma (A): -9.321000 46.39700 x,y,z range (A): 52.78600 52.17800 55.71800 scale (grids/A): 1.916795 object centre (A): 14.28700 -2.366000 18.53800 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : -1.999976 assigned positive charge : 407.5195 centred at (gu) : 89.97874 87.84950 91.80769 assigned negative charge : -409.5207 centred at (gu) : 90.06322 87.74305 92.13663 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25969 grid for indexing accessible points = 1.400000 m= 28996 mr = 54079 m= 5021 mr = 20741 m= 338 mr = 2934 m= 4 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 707 time to turn everything in is 0.7000000 number of dielectric boundary points 37521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20484 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) : 0.6389318 object centre at (A) : 14.28700 -2.366000 18.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2041731E-02 -5.4802764E-02 midg,1,midg; midg,igrid,midg 2.2770561E-02 1.2889797E-02 1,midg,midg; igrid,midg,midg 1.9820824E-02 -2.1313604E-02 gauss-seidel spectral radius is 0.9986796 estimated iterations to convergence 218 setup time was (sec) 1.060000 now iterating at: 19:34:32 rms-change max change #iterations 4.436336 191.7200 at 10iterations 2.086832 72.20710 at 20iterations 0.9920914 31.10398 at 30iterations 0.4666411 14.64966 at 40iterations 0.2212676 6.657862 at 50iterations 0.1048823 3.958605 at 60iterations 4.9681682E-02 1.782774 at 70iterations 2.3557235E-02 0.7101040 at 80iterations 1.1161492E-02 0.3803196 at 90iterations 5.2775214E-03 0.1643062 at 100iterations 2.5124485E-03 8.2569838E-02 at 110iterations 1.1949356E-03 3.7662983E-02 at 120iterations finished qdiffx linear iterations at : 19:34:45 total time elapsed so far: 13.68000 # loops : 120 mean,max change (kT/e) : 1.1949356E-03 3.7662983E-02 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 19:34:45 13.861u 0.473s 0:14.77 97.0% 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 Mon Oct 10 2011 at 19:34:45 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.875193 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): -12.10600 40.68000 ymin,ymax (A): -28.45500 23.72300 zmin,zma (A): -9.321000 46.39700 x,y,z range (A): 52.78600 52.17800 55.71800 scale (grids/A): 2.875193 object centre (A): 14.28700 -2.366000 18.53800 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : -1.999976 assigned positive charge : 407.5195 centred at (gu) : 89.96798 86.77406 92.71143 assigned negative charge : -409.5207 centred at (gu) : 90.09471 86.61457 93.20482 start vw surface at 0.1100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 187092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25969 grid for indexing accessible points = 1.400000 m= 92098 mr = 131839 m= 34990 mr = 73442 m= 8926 mr = 27445 m= 1363 mr = 6498 m= 85 mr = 850 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 2417 time to turn everything in is 1.810000 number of dielectric boundary points 84448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 20774 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) : 1.916795 object centre at (A) : 14.28700 -2.366000 18.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1062459 -0.6553980 midg,1,midg; midg,igrid,midg 0.3171893 0.1746382 1,midg,midg; igrid,midg,midg 0.3967832 -0.2536672 gauss-seidel spectral radius is 0.9992806 estimated iterations to convergence 294 setup time was (sec) 2.210000 now iterating at: 19:34:48 rms-change max change #iterations 10.47179 401.5983 at 10iterations 6.180901 133.6631 at 20iterations 3.625817 69.66409 at 30iterations 2.124314 42.99687 at 40iterations 1.241266 22.57268 at 50iterations 0.7242019 13.37805 at 60iterations 0.4216648 7.463972 at 70iterations 0.2457986 4.998260 at 80iterations 0.1427378 2.824159 at 90iterations 8.2852520E-02 1.492817 at 100iterations 4.8017837E-02 0.8856763 at 110iterations 2.7905542E-02 0.5095882 at 120iterations 1.6186092E-02 0.2832108 at 130iterations 9.3959188E-03 0.1597366 at 140iterations 5.4502445E-03 9.7692490E-02 at 150iterations 3.1656928E-03 5.7018012E-02 at 160iterations 1.8449824E-03 3.4286499E-02 at 170iterations 1.0806445E-03 1.9191742E-02 at 180iterations finished qdiffx linear iterations at : 19:35:09 total time elapsed so far: 23.10000 # loops : 180 mean,max change (kT/e) : 1.0806445E-03 1.9191742E-02 energy calculations done at 23.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.26000 DelPhi exited at 19:35:10 23.269u 0.532s 0:24.23 98.1% 0+0k 0+0io 0pf+0w