Mon Oct 10 13:59:55 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 Mon Oct 10 2011 at 13:59:55 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 = 2577 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: 0.5677649 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): -20.06800 42.63400 ymin,ymax (A): -23.35200 27.95100 zmin,zma (A): -10.09500 37.48100 x,y,z range (A): 62.70200 51.30300 47.57600 scale (grids/A): 0.5677649 object centre (A): 11.28300 2.299500 13.69300 number of atom coordinates read : 2577 total number of charged atoms : 2435 net assigned charge : 4.000008 assigned positive charge : 384.9217 centred at (gu) : 90.44947 90.11757 90.56732 assigned negative charge : -380.9225 centred at (gu) : 90.28127 90.25213 90.62684 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 49496 no. pairs analyzed = 49496 no. exposed pairs = 3750 no. arc points = 26944 no. surface atoms = 1246 nbur = 1331 mkacc time = 0.1300000 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= 235 mr = 2547 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1386160E-09 -2.1317756E-10 midg,1,midg; midg,igrid,midg 2.1549360E-09 -1.1738382E-09 1,midg,midg; igrid,midg,midg -1.4096126E-09 2.9207652E-09 gauss-seidel spectral radius is 0.9839739 estimated iterations to convergence 65 setup time was (sec) 0.7600000 now iterating at: 13:59:57 rms-change max change #iterations 8.0411777E-02 18.01604 at 10iterations 5.8244257E-03 0.9163799 at 20iterations 4.4437585E-04 7.9402924E-02 at 30iterations 3.7922167E-05 6.1855316E-03 at 40iterations 4.9713631E-06 7.4005127E-04 at 50iterations finished qdiffx linear iterations at : 14:00:04 total time elapsed so far: 8.300000 # loops : 50 mean,max change (kT/e) : 4.9713631E-06 7.4005127E-04 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 14:00:07 8.492u 0.731s 0:12.44 74.1% 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 Mon Oct 10 2011 at 14:00:08 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 = 2577 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: 1.703295 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): -20.06800 42.63400 ymin,ymax (A): -23.35200 27.95100 zmin,zma (A): -10.09500 37.48100 x,y,z range (A): 62.70200 51.30300 47.57600 scale (grids/A): 1.703295 object centre (A): 11.28300 2.299500 13.69300 number of atom coordinates read : 2577 total number of charged atoms : 2435 net assigned charge : 4.000008 assigned positive charge : 384.9217 centred at (gu) : 91.34780 90.35204 91.70138 assigned negative charge : -380.9225 centred at (gu) : 90.84386 90.75610 91.88034 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26944 grid for indexing accessible points = 1.400000 m= 17340 mr = 37835 m= 1851 mr = 11114 m= 55 mr = 784 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 814 time to turn everything in is 0.6100000 number of dielectric boundary points 29971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 18849 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) : 0.5677649 object centre at (A) : 11.28300 2.299500 13.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1626226E-02 -9.8502054E-04 midg,1,midg; midg,igrid,midg 1.7213609E-02 -6.2693870E-03 1,midg,midg; igrid,midg,midg -4.3300033E-02 4.7155479E-03 gauss-seidel spectral radius is 0.9983113 estimated iterations to convergence 193 setup time was (sec) 1.130000 now iterating at: 14:00:10 rms-change max change #iterations 3.306406 176.7589 at 10iterations 1.404910 54.86094 at 20iterations 0.5982987 23.49565 at 30iterations 0.2575111 10.03848 at 40iterations 0.1096006 4.580841 at 50iterations 4.7152221E-02 1.682579 at 60iterations 2.0335646E-02 0.7264938 at 70iterations 8.7046036E-03 0.3151984 at 80iterations 3.7256887E-03 0.1379590 at 90iterations 1.6027433E-03 6.8666458E-02 at 100iterations 6.8778673E-04 2.3806095E-02 at 110iterations 2.9666402E-04 1.2105942E-02 at 120iterations finished qdiffx linear iterations at : 14:00:26 total time elapsed so far: 16.30000 # loops : 120 mean,max change (kT/e) : 2.9666402E-04 1.2105942E-02 energy calculations done at 16.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.48000 DelPhi exited at 14:00:29 16.481u 0.897s 0:20.76 83.6% 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 Mon Oct 10 2011 at 14:00:30 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 = 2577 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: 2.554942 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): -20.06800 42.63400 ymin,ymax (A): -23.35200 27.95100 zmin,zma (A): -10.09500 37.48100 x,y,z range (A): 62.70200 51.30300 47.57600 scale (grids/A): 2.554942 object centre (A): 11.28300 2.299500 13.69300 number of atom coordinates read : 2577 total number of charged atoms : 2435 net assigned charge : 4.000008 assigned positive charge : 384.9217 centred at (gu) : 92.02153 90.52782 92.55197 assigned negative charge : -380.9225 centred at (gu) : 91.26573 91.13400 92.82050 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 140362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26944 grid for indexing accessible points = 1.400000 m= 60103 mr = 93688 m= 16579 mr = 45177 m= 2714 mr = 11679 m= 248 mr = 1673 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 2762 time to turn everything in is 1.460000 number of dielectric boundary points 67687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 19470 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) : 1.703295 object centre at (A) : 11.28300 2.299500 13.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1530543 -9.7126160E-03 midg,1,midg; midg,igrid,midg 0.2384173 -6.6431351E-02 1,midg,midg; igrid,midg,midg -0.6743298 -0.2575401 gauss-seidel spectral radius is 0.9991758 estimated iterations to convergence 275 setup time was (sec) 2.100000 now iterating at: 14:00:33 rms-change max change #iterations 8.578878 345.5034 at 10iterations 4.937937 185.2998 at 20iterations 2.817237 75.07407 at 30iterations 1.597749 35.73106 at 40iterations 0.9028743 20.92155 at 50iterations 0.5063789 12.27789 at 60iterations 0.2834923 6.346336 at 70iterations 0.1585146 3.818972 at 80iterations 8.8872783E-02 1.983144 at 90iterations 4.9562570E-02 1.154099 at 100iterations 2.7626498E-02 0.6177063 at 110iterations 1.5389821E-02 0.3411751 at 120iterations 8.5719638E-03 0.1897774 at 130iterations 4.7936761E-03 0.1077144 at 140iterations 2.6682368E-03 5.8414459E-02 at 150iterations 1.4868710E-03 3.3373833E-02 at 160iterations 8.2849187E-04 1.8120766E-02 at 170iterations 4.6081972E-04 1.0236502E-02 at 180iterations finished qdiffx linear iterations at : 14:01:01 total time elapsed so far: 30.23000 # loops : 180 mean,max change (kT/e) : 4.6081972E-04 1.0236502E-02 energy calculations done at 30.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.39000 DelPhi exited at 14:01:02 30.396u 0.881s 0:32.27 96.9% 0+0k 0+0io 0pf+0w