Sun Oct 9 20:03:35 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 Sun Oct 9 2011 at 20:03:35 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5622591 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): 2.929000 65.76300 ymin,ymax (A): -7.745000 54.67200 zmin,zma (A): -1.172000 62.14400 x,y,z range (A): 62.83400 62.41700 63.31600 scale (grids/A): 0.5622591 object centre (A): 34.34600 23.46350 30.48600 number of atom coordinates read : 5005 total number of charged atoms : 4857 net assigned charge : 1.635044 assigned positive charge : 771.7850 centred at (gu) : 87.80576 88.82704 88.93974 assigned negative charge : -770.1556 centred at (gu) : 87.69095 88.80971 88.93565 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10281 nv = 96 ne = 84 npr = 101646 no. pairs analyzed = 101646 no. exposed pairs = 5832 no. arc points = 39201 no. surface atoms = 1975 nbur = 3030 mkacc time = 0.1800000 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 = 1.540000 m= 447 mr = 5892 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4002 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13472 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1559625E-10 2.6163025E-10 midg,1,midg; midg,igrid,midg -1.4415248E-10 4.5935059E-10 1,midg,midg; igrid,midg,midg -3.7114751E-09 1.5227670E-09 gauss-seidel spectral radius is 0.9838307 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 20:03:35 rms-change max change #iterations 0.1174943 15.49581 at 10iterations 1.1081314E-02 1.379349 at 20iterations 3.3464336E-03 0.3851318 at 30iterations 1.6138796E-03 0.1956077 at 40iterations 8.0535823E-04 0.1018624 at 50iterations finished qdiffx linear iterations at : 20:03:38 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.0535823E-04 0.1018624 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 20:03:39 3.548u 0.181s 0:04.01 92.7% 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 Sun Oct 9 2011 at 20:03:39 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.686777 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): 2.929000 65.76300 ymin,ymax (A): -7.745000 54.67200 zmin,zma (A): -1.172000 62.14400 x,y,z range (A): 62.83400 62.41700 63.31600 scale (grids/A): 1.686777 object centre (A): 34.34600 23.46350 30.48600 number of atom coordinates read : 5005 total number of charged atoms : 4857 net assigned charge : 1.635044 assigned positive charge : 771.7850 centred at (gu) : 83.41608 86.47990 86.81780 assigned negative charge : -770.1556 centred at (gu) : 83.07285 86.42910 86.80685 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 114608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39201 grid for indexing accessible points = 1.400000 m= 41132 mr = 83387 m= 5283 mr = 29971 m= 186 mr = 2928 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 249 time to turn everything in is 0.5500000 number of dielectric boundary points 44892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 37415 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) : 0.5622591 object centre at (A) : 34.34600 23.46350 30.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9902687E-02 -2.9965194E-02 midg,1,midg; midg,igrid,midg 1.5313545E-02 1.3167171E-02 1,midg,midg; igrid,midg,midg -2.2901261E-02 4.2591181E-02 gauss-seidel spectral radius is 0.9984831 estimated iterations to convergence 204 setup time was (sec) 0.7700000 now iterating at: 20:03:40 rms-change max change #iterations 4.959122 186.3793 at 10iterations 2.226230 59.79057 at 20iterations 1.003312 29.40760 at 30iterations 0.4519947 11.81063 at 40iterations 0.2043737 5.737062 at 50iterations 9.2393182E-02 2.671013 at 60iterations 4.2164713E-02 1.155602 at 70iterations 1.9679828E-02 0.5370026 at 80iterations 9.8263668E-03 0.2829819 at 90iterations 5.4742782E-03 0.1637726 at 100iterations 3.5141821E-03 9.7154617E-02 at 110iterations 2.5262479E-03 7.2097778E-02 at 120iterations finished qdiffx linear iterations at : 20:03:47 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 2.5262479E-03 7.2097778E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 20:03:47 8.147u 0.205s 0:08.63 96.6% 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 Sun Oct 9 2011 at 20:03:47 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.530166 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): 2.929000 65.76300 ymin,ymax (A): -7.745000 54.67200 zmin,zma (A): -1.172000 62.14400 x,y,z range (A): 62.83400 62.41700 63.31600 scale (grids/A): 2.530166 object centre (A): 34.34600 23.46350 30.48600 number of atom coordinates read : 5005 total number of charged atoms : 4857 net assigned charge : 1.635044 assigned positive charge : 771.7850 centred at (gu) : 80.12367 84.71931 85.22640 assigned negative charge : -770.1556 centred at (gu) : 79.60934 84.64365 85.21026 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 265907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39201 grid for indexing accessible points = 1.400000 m= 136456 mr = 201694 m= 45300 mr = 112056 m= 8726 mr = 35652 m= 834 mr = 6087 m= 17 mr = 468 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 1.410000 number of dielectric boundary points 101283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 38829 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) : 1.686777 object centre at (A) : 34.34600 23.46350 30.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5581979 -0.7585779 midg,1,midg; midg,igrid,midg -2.5599713E-02 8.5346572E-02 1,midg,midg; igrid,midg,midg -0.4663464 0.7446954 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 1.650000 now iterating at: 20:03:49 rms-change max change #iterations 12.42106 348.4438 at 10iterations 7.351019 147.7880 at 20iterations 4.315052 86.17583 at 30iterations 2.529330 46.12716 at 40iterations 1.473084 25.15995 at 50iterations 0.8575156 14.64292 at 60iterations 0.4979576 7.689942 at 70iterations 0.2889592 4.563389 at 80iterations 0.1674185 2.965553 at 90iterations 9.6783660E-02 1.471323 at 100iterations 5.6117360E-02 0.9380226 at 110iterations 3.2703515E-02 0.5058136 at 120iterations 1.9266628E-02 0.3171902 at 130iterations 1.1539554E-02 0.1922340 at 140iterations 7.2068344E-03 0.1250496 at 150iterations 4.7631352E-03 8.2883835E-02 at 160iterations 3.3999812E-03 6.4563751E-02 at 170iterations 2.6120259E-03 4.2469978E-02 at 180iterations finished qdiffx linear iterations at : 20:04:01 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 2.6120259E-03 4.2469978E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 20:04:01 13.571u 0.208s 0:14.08 97.7% 0+0k 0+0io 0pf+0w