Tue Oct 11 06:05:21 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 06:05:21 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7419140 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): -18.09100 29.89300 ymin,ymax (A): -11.78100 30.99800 zmin,zma (A): -8.529000 38.19800 x,y,z range (A): 47.98400 42.77900 46.72700 scale (grids/A): 0.7419140 object centre (A): 5.901000 9.608500 14.83450 number of atom coordinates read : 2061 total number of charged atoms : 1931 net assigned charge : 6.039010 assigned positive charge : 314.5461 centred at (gu) : 90.08907 89.58656 90.97557 assigned negative charge : -308.5071 centred at (gu) : 90.01875 89.49693 90.86605 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7928 nv = 96 ne = 84 npr = 41244 no. pairs analyzed = 41244 no. exposed pairs = 2501 no. arc points = 17116 no. surface atoms = 846 nbur = 1215 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 607 mr = 4722 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2800000 number of dielectric boundary points 3698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1501 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8286 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9812214E-10 2.6444317E-07 midg,1,midg; midg,igrid,midg 1.9021039E-08 1.8583674E-07 1,midg,midg; igrid,midg,midg 3.7548826E-08 1.8421510E-07 gauss-seidel spectral radius is 0.9905218 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 06:05:22 rms-change max change #iterations 0.2469605 33.88262 at 10iterations 3.4276482E-02 4.776024 at 20iterations 4.8890128E-03 0.6801300 at 30iterations 8.4869011E-04 9.5474243E-02 at 40iterations 2.0831714E-04 2.2743225E-02 at 50iterations finished qdiffx linear iterations at : 06:05:25 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.0831714E-04 2.2743225E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 06:05:25 3.501u 0.191s 0:04.14 89.1% 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 06:05:25 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.225742 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): -18.09100 29.89300 ymin,ymax (A): -11.78100 30.99800 zmin,zma (A): -8.529000 38.19800 x,y,z range (A): 47.98400 42.77900 46.72700 scale (grids/A): 2.225742 object centre (A): 5.901000 9.608500 14.83450 number of atom coordinates read : 2061 total number of charged atoms : 1931 net assigned charge : 6.039010 assigned positive charge : 314.5461 centred at (gu) : 90.26737 88.75983 92.92671 assigned negative charge : -308.5071 centred at (gu) : 90.05623 88.49086 92.59824 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 82995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17116 grid for indexing accessible points = 1.400000 m= 35614 mr = 59752 m= 7733 mr = 27865 m= 812 mr = 5340 m= 37 mr = 477 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 219 time to turn everything in is 0.6800000 number of dielectric boundary points 33750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15370 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) : 0.7419140 object centre at (A) : 5.901000 9.608500 14.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4931948E-02 4.3150604E-02 midg,1,midg; midg,igrid,midg 3.3817649E-02 3.0948741E-02 1,midg,midg; igrid,midg,midg 4.9090315E-02 3.5119608E-02 gauss-seidel spectral radius is 0.9989206 estimated iterations to convergence 241 setup time was (sec) 1.000000 now iterating at: 06:05:27 rms-change max change #iterations 5.021744 207.7976 at 10iterations 2.552768 77.21596 at 20iterations 1.303058 37.82847 at 30iterations 0.6639271 20.72196 at 40iterations 0.3384317 9.465052 at 50iterations 0.1732328 5.291824 at 60iterations 8.8480875E-02 2.529175 at 70iterations 4.5267086E-02 1.359505 at 80iterations 2.3255672E-02 0.6853485 at 90iterations 1.2043767E-02 0.3611693 at 100iterations 6.2611667E-03 0.1760721 at 110iterations 3.3126306E-03 9.8834991E-02 at 120iterations finished qdiffx linear iterations at : 06:05:35 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 3.3126306E-03 9.8834991E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 06:05:35 9.327u 0.211s 0:09.95 95.7% 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 Tue Oct 11 2011 at 06:05:35 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.338613 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): -18.09100 29.89300 ymin,ymax (A): -11.78100 30.99800 zmin,zma (A): -8.529000 38.19800 x,y,z range (A): 47.98400 42.77900 46.72700 scale (grids/A): 3.338613 object centre (A): 5.901000 9.608500 14.83450 number of atom coordinates read : 2061 total number of charged atoms : 1931 net assigned charge : 6.039010 assigned positive charge : 314.5461 centred at (gu) : 90.40092 88.13975 94.39034 assigned negative charge : -308.5071 centred at (gu) : 90.08434 87.73628 93.89737 start vw surface at 0.1300000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 190834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17116 grid for indexing accessible points = 1.400000 m= 108322 mr = 143118 m= 47584 mr = 91533 m= 14999 mr = 40136 m= 3400 mr = 11977 m= 537 mr = 2537 m= 32 mr = 373 m= 0 mr = 13 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 2.060000 number of dielectric boundary points 76021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 15448 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) : 2.225742 object centre at (A) : 5.901000 9.608500 14.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4834364 0.4300129 midg,1,midg; midg,igrid,midg 0.2779166 0.1775565 1,midg,midg; igrid,midg,midg 0.2691748 0.1341279 gauss-seidel spectral radius is 0.9993200 estimated iterations to convergence 303 setup time was (sec) 2.390000 now iterating at: 06:05:38 rms-change max change #iterations 10.92225 305.8110 at 10iterations 6.534060 139.7864 at 20iterations 3.894758 74.53508 at 30iterations 2.321768 39.09166 at 40iterations 1.379827 25.22306 at 50iterations 0.8185982 13.63855 at 60iterations 0.4853651 9.066499 at 70iterations 0.2881024 4.856308 at 80iterations 0.1704298 2.795722 at 90iterations 0.1008828 1.622227 at 100iterations 5.9971370E-02 1.016668 at 110iterations 3.5737086E-02 0.5915985 at 120iterations 2.1522237E-02 0.3984604 at 130iterations 1.3198486E-02 0.2207413 at 140iterations 8.3419010E-03 0.1516113 at 150iterations 5.5073802E-03 0.1030884 at 160iterations 3.8443324E-03 6.9328308E-02 at 170iterations 2.8525887E-03 5.2970886E-02 at 180iterations finished qdiffx linear iterations at : 06:05:49 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 2.8525887E-03 5.2970886E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 06:05:50 13.512u 0.226s 0:14.23 96.4% 0+0k 0+0io 0pf+0w