Mon Oct 10 17:00:56 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 Mon Oct 10 2011 at 17:00:56 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.5769948 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): -31.14700 30.55200 ymin,ymax (A): -21.15700 25.60000 zmin,zma (A): -7.448000 39.72700 x,y,z range (A): 61.69900 46.75700 47.17500 scale (grids/A): 0.5769948 object centre (A): -0.2974997 2.221500 16.13950 number of atom coordinates read : 2687 total number of charged atoms : 2545 net assigned charge : -4.485965 assigned positive charge : 401.9155 centred at (gu) : 90.35597 90.28555 89.40322 assigned negative charge : -406.4024 centred at (gu) : 90.42595 90.06443 89.34969 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5853 nv = 96 ne = 84 npr = 53732 no. pairs analyzed = 53732 no. exposed pairs = 3492 no. arc points = 24597 no. surface atoms = 1189 nbur = 1498 mkacc time = 9.0000004E-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 = 1.512000 m= 229 mr = 3022 m= 0 mr = 4 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2465 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7513 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1392861E-09 7.3242037E-11 midg,1,midg; midg,igrid,midg -4.6853565E-09 3.2629877E-09 1,midg,midg; igrid,midg,midg 3.5087802E-10 -2.3524431E-09 gauss-seidel spectral radius is 0.9844773 estimated iterations to convergence 66 setup time was (sec) 0.3800000 now iterating at: 17:00:57 rms-change max change #iterations 9.3132660E-02 16.93124 at 10iterations 7.1484703E-03 1.306976 at 20iterations 5.5779889E-04 8.8954926E-02 at 30iterations 4.2437397E-05 6.8435669E-03 at 40iterations 3.8728663E-06 6.5803528E-04 at 50iterations finished qdiffx linear iterations at : 17:01:00 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.8728663E-06 6.5803528E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 17:01:01 3.330u 0.174s 0:04.52 77.4% 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 17:01:01 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.730984 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): -31.14700 30.55200 ymin,ymax (A): -21.15700 25.60000 zmin,zma (A): -7.448000 39.72700 x,y,z range (A): 61.69900 46.75700 47.17500 scale (grids/A): 1.730984 object centre (A): -0.2974997 2.221500 16.13950 number of atom coordinates read : 2687 total number of charged atoms : 2545 net assigned charge : -4.485965 assigned positive charge : 401.9155 centred at (gu) : 91.06744 90.85582 88.20876 assigned negative charge : -406.4024 centred at (gu) : 91.27766 90.19308 88.04881 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24597 grid for indexing accessible points = 1.400000 m= 20207 mr = 43288 m= 2258 mr = 13977 m= 60 mr = 1195 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 688 time to turn everything in is 0.3100000 number of dielectric boundary points 28689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19830 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) : 0.5769948 object centre at (A) : -0.2974997 2.221500 16.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8776425E-03 -3.9627184E-03 midg,1,midg; midg,igrid,midg -2.5440166E-02 1.2876858E-02 1,midg,midg; igrid,midg,midg 8.3654560E-03 -1.7465879E-03 gauss-seidel spectral radius is 0.9983633 estimated iterations to convergence 196 setup time was (sec) 0.5300000 now iterating at: 17:01:02 rms-change max change #iterations 3.584456 149.2081 at 10iterations 1.550782 61.05915 at 20iterations 0.6746516 23.30542 at 30iterations 0.2949495 10.71630 at 40iterations 0.1281169 4.427326 at 50iterations 5.5824533E-02 2.187186 at 60iterations 2.4278402E-02 0.8812685 at 70iterations 1.0564079E-02 0.3789648 at 80iterations 4.6160226E-03 0.2222641 at 90iterations 2.0168764E-03 7.0642471E-02 at 100iterations 8.7373803E-04 3.1445742E-02 at 110iterations 3.8180983E-04 1.2709618E-02 at 120iterations finished qdiffx linear iterations at : 17:01:09 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 3.8180983E-04 1.2709618E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 17:01:10 7.554u 0.180s 0:08.54 90.5% 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 17:01:10 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.596477 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): -31.14700 30.55200 ymin,ymax (A): -21.15700 25.60000 zmin,zma (A): -7.448000 39.72700 x,y,z range (A): 61.69900 46.75700 47.17500 scale (grids/A): 2.596477 object centre (A): -0.2974997 2.221500 16.13950 number of atom coordinates read : 2687 total number of charged atoms : 2545 net assigned charge : -4.485965 assigned positive charge : 401.9155 centred at (gu) : 91.60102 91.28368 87.31294 assigned negative charge : -406.4024 centred at (gu) : 91.91625 90.28950 87.07316 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150269 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24597 grid for indexing accessible points = 1.400000 m= 68825 mr = 106344 m= 20574 mr = 54116 m= 3541 mr = 15752 m= 282 mr = 2394 m= 6 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2434 time to turn everything in is 0.7800000 number of dielectric boundary points 64745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20352 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) : 1.730984 object centre at (A) : -0.2974997 2.221500 16.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6701095E-02 -5.9286881E-02 midg,1,midg; midg,igrid,midg -0.2918354 0.1920516 1,midg,midg; igrid,midg,midg 0.3792087 5.4184332E-02 gauss-seidel spectral radius is 0.9991915 estimated iterations to convergence 278 setup time was (sec) 1.010000 now iterating at: 17:01:11 rms-change max change #iterations 9.058668 326.8706 at 10iterations 5.193336 137.2658 at 20iterations 2.947231 69.51508 at 30iterations 1.667980 42.38081 at 40iterations 0.9439338 24.08908 at 50iterations 0.5323954 11.96611 at 60iterations 0.2987993 6.709202 at 70iterations 0.1679732 4.127624 at 80iterations 9.4338693E-02 1.941345 at 90iterations 5.2928876E-02 1.075740 at 100iterations 2.9657360E-02 0.5606899 at 110iterations 1.6566100E-02 0.3341246 at 120iterations 9.3021262E-03 0.1934357 at 130iterations 5.2031414E-03 0.1138668 at 140iterations 2.9250688E-03 6.0749054E-02 at 150iterations 1.6328347E-03 3.5421371E-02 at 160iterations 9.1160042E-04 1.8093109E-02 at 170iterations 5.1066896E-04 1.0262489E-02 at 180iterations finished qdiffx linear iterations at : 17:01:22 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 5.1066896E-04 1.0262489E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 17:01:23 11.987u 0.202s 0:13.43 90.6% 0+0k 0+0io 0pf+0w