Sat Oct 15 11:27:43 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 Sat Oct 15 2011 at 11:27:43 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN8 803 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6188076 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): -31.31100 17.54300 ymin,ymax (A): -23.65300 23.26200 zmin,zma (A): -12.41100 45.11900 x,y,z range (A): 48.85400 46.91500 57.53000 scale (grids/A): 0.6188076 object centre (A): -6.884001 -0.1955004 16.35400 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 88.41684 89.08405 89.59598 assigned negative charge : -389.0045 centred at (gu) : 88.31882 89.13763 89.46748 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6391 nv = 96 ne = 84 npr = 53841 no. pairs analyzed = 53841 no. exposed pairs = 2971 no. arc points = 21416 no. surface atoms = 1001 nbur = 1577 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3559 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.1900000 number of dielectric boundary points 3120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2155 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8013 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6459033E-09 1.0367184E-08 midg,1,midg; midg,igrid,midg 8.1160154E-09 -1.6591117E-10 1,midg,midg; igrid,midg,midg -4.5782329E-09 6.6696262E-09 gauss-seidel spectral radius is 0.9864701 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 11:27:44 rms-change max change #iterations 0.1263741 19.84627 at 10iterations 1.1675830E-02 1.556110 at 20iterations 1.0756606E-03 0.1701584 at 30iterations 1.0142502E-04 1.3542175E-02 at 40iterations 9.4517300E-06 1.2340546E-03 at 50iterations finished qdiffx linear iterations at : 11:27:47 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 9.4517300E-06 1.2340546E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 11:27:48 3.567u 0.216s 0:04.57 82.4% 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 Sat Oct 15 2011 at 11:27:48 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN8 803 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.856423 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): -31.31100 17.54300 ymin,ymax (A): -23.65300 23.26200 zmin,zma (A): -12.41100 45.11900 x,y,z range (A): 48.85400 46.91500 57.53000 scale (grids/A): 1.856423 object centre (A): -6.884001 -0.1955004 16.35400 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 85.25005 87.25166 88.78722 assigned negative charge : -389.0045 centred at (gu) : 84.95623 87.41280 88.40209 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21416 grid for indexing accessible points = 1.400000 m= 23834 mr = 48549 m= 3332 mr = 17547 m= 152 mr = 2047 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3855 time to turn everything in is 0.3700000 number of dielectric boundary points 28691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19272 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) : 0.6188076 object centre at (A) : -6.884001 -0.1955004 16.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6571911E-02 2.7595591E-02 midg,1,midg; midg,igrid,midg 1.2910629E-02 1.0280387E-03 1,midg,midg; igrid,midg,midg -2.9731912E-03 2.9359626E-02 gauss-seidel spectral radius is 0.9985581 estimated iterations to convergence 209 setup time was (sec) 0.6300000 now iterating at: 11:27:49 rms-change max change #iterations 4.042197 161.9526 at 10iterations 1.846150 62.67082 at 20iterations 0.8473613 30.20729 at 30iterations 0.3896211 17.39741 at 40iterations 0.1786668 5.711006 at 50iterations 8.1903793E-02 2.808750 at 60iterations 3.7607677E-02 1.269892 at 70iterations 1.7215662E-02 0.5539756 at 80iterations 7.9025263E-03 0.2588258 at 90iterations 3.6308500E-03 0.1131382 at 100iterations 1.6716955E-03 5.5171967E-02 at 110iterations 7.6353672E-04 2.8575897E-02 at 120iterations finished qdiffx linear iterations at : 11:28:00 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 7.6353672E-04 2.8575897E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.42000 DelPhi exited at 11:28:01 10.426u 0.321s 0:13.26 80.9% 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 Sat Oct 15 2011 at 11:28:01 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN8 803 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.784634 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): -31.31100 17.54300 ymin,ymax (A): -23.65300 23.26200 zmin,zma (A): -12.41100 45.11900 x,y,z range (A): 48.85400 46.91500 57.53000 scale (grids/A): 2.784634 object centre (A): -6.884001 -0.1955004 16.35400 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 82.87486 85.87735 88.18067 assigned negative charge : -389.0045 centred at (gu) : 82.43431 86.11900 87.60315 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 161427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21416 grid for indexing accessible points = 1.400000 m= 79151 mr = 117674 m= 26346 mr = 65151 m= 5792 mr = 21179 m= 655 mr = 4305 m= 29 mr = 422 m= 0 mr = 6 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 13059 time to turn everything in is 0.9100000 number of dielectric boundary points 64663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19630 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) : 1.856423 object centre at (A) : -6.884001 -0.1955004 16.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8330562E-02 0.3572901 midg,1,midg; midg,igrid,midg 0.1675076 1.0955255E-02 1,midg,midg; igrid,midg,midg -3.1475201E-02 0.3841785 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.210000 now iterating at: 11:28:03 rms-change max change #iterations 9.490611 296.8064 at 10iterations 5.442581 114.4400 at 20iterations 3.104267 65.21207 at 30iterations 1.771049 33.44017 at 40iterations 1.006994 18.81821 at 50iterations 0.5734169 12.24990 at 60iterations 0.3268519 6.247612 at 70iterations 0.1850477 3.402017 at 80iterations 0.1054368 2.335840 at 90iterations 5.9941951E-02 1.200380 at 100iterations 3.4000512E-02 0.7590075 at 110iterations 1.9305142E-02 0.3578491 at 120iterations 1.0975047E-02 0.2074890 at 130iterations 6.2456760E-03 0.1221657 at 140iterations 3.5504878E-03 7.0638657E-02 at 150iterations 2.0220249E-03 3.8104057E-02 at 160iterations 1.1525517E-03 2.2631168E-02 at 170iterations 6.5712142E-04 1.2265205E-02 at 180iterations finished qdiffx linear iterations at : 11:28:21 total time elapsed so far: 15.98000 # loops : 180 mean,max change (kT/e) : 6.5712142E-04 1.2265205E-02 energy calculations done at 15.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 11:28:21 16.110u 0.314s 0:19.70 83.3% 0+0k 0+0io 0pf+0w