Sat Oct 15 11:35:39 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 Sat Oct 15 2011 at 11:35:39 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3723 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: 0.5486968 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): -3.375000 60.41100 ymin,ymax (A): -18.51300 44.49700 zmin,zma (A): -5.592000 59.28900 x,y,z range (A): 63.78600 63.01000 64.88100 scale (grids/A): 0.5486968 object centre (A): 28.51800 12.99200 26.84850 number of atom coordinates read : 3723 total number of charged atoms : 3573 net assigned charge : -7.499969 assigned positive charge : 565.0646 centred at (gu) : 89.06238 86.77145 90.45794 assigned negative charge : -572.5668 centred at (gu) : 89.12652 86.75031 90.45554 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7364 nv = 96 ne = 84 npr = 74436 no. pairs analyzed = 74436 no. exposed pairs = 4871 no. arc points = 33841 no. surface atoms = 1617 nbur = 2106 mkacc time = 0.1900000 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 = 1.568000 m= 306 mr = 3803 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3466 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7790877E-10 -5.4491955E-10 midg,1,midg; midg,igrid,midg -1.5727186E-09 -1.5064128E-10 1,midg,midg; igrid,midg,midg 1.1183328E-10 -8.8619972E-10 gauss-seidel spectral radius is 0.9829332 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 11:35:40 rms-change max change #iterations 8.4729739E-02 13.05572 at 10iterations 5.8455230E-03 1.010090 at 20iterations 4.3711529E-04 6.1995983E-02 at 30iterations 6.0663639E-05 9.5744133E-03 at 40iterations 1.4884422E-05 2.5014877E-03 at 50iterations finished qdiffx linear iterations at : 11:35:44 total time elapsed so far: 5.240000 # loops : 50 mean,max change (kT/e) : 1.4884422E-05 2.5014877E-03 energy calculations done at 5.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.410000 DelPhi exited at 11:35:45 5.418u 0.467s 0:06.16 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 Sat Oct 15 2011 at 11:35:45 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3723 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: 1.646090 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): -3.375000 60.41100 ymin,ymax (A): -18.51300 44.49700 zmin,zma (A): -5.592000 59.28900 x,y,z range (A): 63.78600 63.01000 64.88100 scale (grids/A): 1.646090 object centre (A): 28.51800 12.99200 26.84850 number of atom coordinates read : 3723 total number of charged atoms : 3573 net assigned charge : -7.499969 assigned positive charge : 565.0646 centred at (gu) : 87.18636 80.31322 91.37288 assigned negative charge : -572.5668 centred at (gu) : 87.37918 80.25018 91.36588 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33841 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25475 mr = 55918 m= 2703 mr = 17195 m= 72 mr = 1268 m= 0 mr = 4 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.7100000 number of dielectric boundary points 35793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 27457 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) : 0.5486968 object centre at (A) : 28.51800 12.99200 26.84850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4428907E-03 4.7588469E-03 midg,1,midg; midg,igrid,midg -3.2687366E-02 -6.1841044E-03 1,midg,midg; igrid,midg,midg -6.9445870E-03 -3.1366467E-02 gauss-seidel spectral radius is 0.9982832 estimated iterations to convergence 192 setup time was (sec) 1.060000 now iterating at: 11:35:46 rms-change max change #iterations 3.880493 154.3280 at 10iterations 1.657096 60.49967 at 20iterations 0.7057778 23.43460 at 30iterations 0.3010260 10.57737 at 40iterations 0.1288453 4.353947 at 50iterations 5.4851431E-02 1.905529 at 60iterations 2.3474272E-02 0.8113823 at 70iterations 1.0042391E-02 0.3028207 at 80iterations 4.2980337E-03 0.1572800 at 90iterations 1.8463142E-03 5.9099197E-02 at 100iterations 7.8955264E-04 3.0073166E-02 at 110iterations 3.4303201E-04 1.1463165E-02 at 120iterations finished qdiffx linear iterations at : 11:35:58 total time elapsed so far: 12.95000 # loops : 120 mean,max change (kT/e) : 3.4303201E-04 1.1463165E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 11:35:59 13.114u 0.537s 0:13.92 97.9% 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 Sat Oct 15 2011 at 11:35:59 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3723 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: 2.469136 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): -3.375000 60.41100 ymin,ymax (A): -18.51300 44.49700 zmin,zma (A): -5.592000 59.28900 x,y,z range (A): 63.78600 63.01000 64.88100 scale (grids/A): 2.469136 object centre (A): 28.51800 12.99200 26.84850 number of atom coordinates read : 3723 total number of charged atoms : 3573 net assigned charge : -7.499969 assigned positive charge : 565.0646 centred at (gu) : 85.77934 75.46961 92.05915 assigned negative charge : -572.5668 centred at (gu) : 86.06855 75.37535 92.04875 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 190168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33841 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 88853 mr = 136872 m= 24918 mr = 69743 m= 4042 mr = 18255 m= 272 mr = 2571 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 382 time to turn everything in is 1.750000 number of dielectric boundary points 80728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 28522 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) : 1.646090 object centre at (A) : 28.51800 12.99200 26.84850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8425996E-03 0.4016942 midg,1,midg; midg,igrid,midg -0.6229460 -9.3441471E-02 1,midg,midg; igrid,midg,midg -0.1377575 -0.6131305 gauss-seidel spectral radius is 0.9991825 estimated iterations to convergence 276 setup time was (sec) 2.160000 now iterating at: 11:36:02 rms-change max change #iterations 10.05735 259.3477 at 10iterations 5.725900 153.3083 at 20iterations 3.260911 71.59981 at 30iterations 1.845160 37.07572 at 40iterations 1.040771 21.37771 at 50iterations 0.5865219 13.26883 at 60iterations 0.3292992 6.497493 at 70iterations 0.1845198 3.803981 at 80iterations 0.1035521 1.947873 at 90iterations 5.7741284E-02 1.205475 at 100iterations 3.2418247E-02 0.6403236 at 110iterations 1.8161345E-02 0.3355498 at 120iterations 1.0145584E-02 0.1910162 at 130iterations 5.6786905E-03 0.1040993 at 140iterations 3.1810640E-03 6.6696167E-02 at 150iterations 1.7802424E-03 3.1611443E-02 at 160iterations 1.0026778E-03 1.9645691E-02 at 170iterations 5.6639465E-04 1.1681557E-02 at 180iterations finished qdiffx linear iterations at : 11:36:22 total time elapsed so far: 22.15000 # loops : 180 mean,max change (kT/e) : 5.6639465E-04 1.1681557E-02 energy calculations done at 22.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.31000 DelPhi exited at 11:36:22 22.311u 0.574s 0:23.19 98.6% 0+0k 0+0io 0pf+0w