Tue Oct 11 01:34:24 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 Tue Oct 11 2011 at 01:34:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3934 !!! WARNING: MG5 571 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5195184 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): -12.80800 53.20600 ymin,ymax (A): 0.6209999 65.15400 zmin,zma (A): -17.57800 50.94700 x,y,z range (A): 66.01400 64.53300 68.52500 scale (grids/A): 0.5195184 object centre (A): 20.19900 32.88750 16.68450 number of atom coordinates read : 3934 total number of charged atoms : 3782 net assigned charge : 7.400031 assigned positive charge : 602.6582 centred at (gu) : 90.62335 90.18215 88.17383 assigned negative charge : -595.2606 centred at (gu) : 90.75901 90.28580 88.22628 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6879 nv = 96 ne = 84 npr = 77117 no. pairs analyzed = 77117 no. exposed pairs = 5040 no. arc points = 35683 no. surface atoms = 1690 nbur = 2244 mkacc time = 0.2200000 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 = 1.652000 m= 246 mr = 3478 m= 0 mr = 12 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.4600000 number of dielectric boundary points 3635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3502 ## 502 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9051 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1268634E-10 -4.1326942E-12 midg,1,midg; midg,igrid,midg 4.5362869E-10 -1.8247938E-10 1,midg,midg; igrid,midg,midg 4.8726501E-10 -3.2808717E-10 gauss-seidel spectral radius is 0.9809933 estimated iterations to convergence 60 setup time was (sec) 0.7200000 now iterating at: 01:34:25 rms-change max change #iterations 6.5143317E-02 10.63766 at 10iterations 4.4507617E-03 0.8926563 at 20iterations 6.3314161E-04 0.1787224 at 30iterations 1.4168279E-04 4.3205261E-02 at 40iterations 3.3995271E-05 1.0444641E-02 at 50iterations finished qdiffx linear iterations at : 01:34:29 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 3.3995271E-05 1.0444641E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 01:34:31 4.272u 0.284s 0:06.60 68.9% 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 Tue Oct 11 2011 at 01:34:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3934 !!! WARNING: MG5 571 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.558555 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): -12.80800 53.20600 ymin,ymax (A): 0.6209999 65.15400 zmin,zma (A): -17.57800 50.94700 x,y,z range (A): 66.01400 64.53300 68.52500 scale (grids/A): 1.558555 object centre (A): 20.19900 32.88750 16.68450 number of atom coordinates read : 3934 total number of charged atoms : 3782 net assigned charge : 7.400031 assigned positive charge : 602.6582 centred at (gu) : 91.86881 90.54531 84.52011 assigned negative charge : -595.2606 centred at (gu) : 92.27669 90.85696 84.67825 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21598 mr = 51709 m= 1834 mr = 14203 m= 31 mr = 792 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1962 time to turn everything in is 0.6900000 number of dielectric boundary points 33931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 28535 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) : 0.5195184 object centre at (A) : 20.19900 32.88750 16.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1933196E-03 -3.0588109E-02 midg,1,midg; midg,igrid,midg 2.2234938E-03 3.7458180E-03 1,midg,midg; igrid,midg,midg 2.3634547E-02 1.2596281E-02 gauss-seidel spectral radius is 0.9980898 estimated iterations to convergence 182 setup time was (sec) 1.000000 now iterating at: 01:34:33 rms-change max change #iterations 3.547769 148.0095 at 10iterations 1.433221 53.59063 at 20iterations 0.5833042 19.02334 at 30iterations 0.2391074 8.193126 at 40iterations 9.7157776E-02 3.417556 at 50iterations 3.9638527E-02 1.306461 at 60iterations 1.6250607E-02 0.5448475 at 70iterations 6.6575892E-03 0.2385635 at 80iterations 2.7789313E-03 9.6961975E-02 at 90iterations 1.1861575E-03 4.9892426E-02 at 100iterations 5.1701668E-04 2.2106171E-02 at 110iterations 2.3438205E-04 1.1719942E-02 at 120iterations finished qdiffx linear iterations at : 01:34:42 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 2.3438205E-04 1.1719942E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 01:34:43 9.655u 0.303s 0:11.29 88.1% 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 01:34:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3934 !!! WARNING: MG5 571 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.337833 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): -12.80800 53.20600 ymin,ymax (A): 0.6209999 65.15400 zmin,zma (A): -17.57800 50.94700 x,y,z range (A): 66.01400 64.53300 68.52500 scale (grids/A): 2.337833 object centre (A): 20.19900 32.88750 16.68450 number of atom coordinates read : 3934 total number of charged atoms : 3782 net assigned charge : 7.400031 assigned positive charge : 602.6582 centred at (gu) : 92.80296 90.81754 81.77977 assigned negative charge : -595.2606 centred at (gu) : 93.41509 91.28521 82.01729 start vw surface at 0.2100000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 179760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 77274 mr = 127373 m= 19414 mr = 59647 m= 2650 mr = 14172 m= 104 mr = 1579 m= 0 mr = 24 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 7057 time to turn everything in is 1.670000 number of dielectric boundary points 76407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 30189 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) : 1.558555 object centre at (A) : 20.19900 32.88750 16.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1969011E-05 -0.4574170 midg,1,midg; midg,igrid,midg 9.7052038E-02 0.1904528 1,midg,midg; igrid,midg,midg 0.3533534 0.1931541 gauss-seidel spectral radius is 0.9991277 estimated iterations to convergence 267 setup time was (sec) 2.020000 now iterating at: 01:34:45 rms-change max change #iterations 9.481765 275.7619 at 10iterations 5.330497 137.4402 at 20iterations 2.977211 65.81760 at 30iterations 1.653522 35.88935 at 40iterations 0.9138588 19.77191 at 50iterations 0.5044139 11.31704 at 60iterations 0.2778322 5.666193 at 70iterations 0.1530649 3.380043 at 80iterations 8.4316522E-02 1.747245 at 90iterations 4.6191659E-02 0.8573723 at 100iterations 2.5406621E-02 0.5016289 at 110iterations 1.3954043E-02 0.3147545 at 120iterations 7.6782592E-03 0.1605568 at 130iterations 4.2450442E-03 8.3051682E-02 at 140iterations 2.3557420E-03 5.5685043E-02 at 150iterations 1.3148919E-03 2.6786804E-02 at 160iterations 7.4319699E-04 1.7265320E-02 at 170iterations 4.2667636E-04 1.1383057E-02 at 180iterations finished qdiffx linear iterations at : 01:34:59 total time elapsed so far: 16.09000 # loops : 180 mean,max change (kT/e) : 4.2667636E-04 1.1383057E-02 energy calculations done at 16.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.27000 DelPhi exited at 01:35:00 16.275u 0.312s 0:16.93 97.9% 0+0k 0+0io 0pf+0w