Sun Oct 9 23:12:34 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 Sun Oct 9 2011 at 23:12:34 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 = 2169 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: 0.6987653 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): -11.99000 31.73200 ymin,ymax (A): -22.31400 28.52900 zmin,zma (A): -9.874001 41.07300 x,y,z range (A): 43.72200 50.84300 50.94700 scale (grids/A): 0.6987653 object centre (A): 9.871000 3.107500 15.59950 number of atom coordinates read : 2169 total number of charged atoms : 2030 net assigned charge : 0.5000094 assigned positive charge : 316.5767 centred at (gu) : 92.03680 90.90601 90.93861 assigned negative charge : -316.0769 centred at (gu) : 91.98924 90.86283 90.64590 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7628 nv = 96 ne = 84 npr = 42062 no. pairs analyzed = 42062 no. exposed pairs = 2829 no. arc points = 20002 no. surface atoms = 963 nbur = 1206 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4219 m= 1 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0082703E-07 1.4289161E-07 midg,1,midg; midg,igrid,midg -1.3344808E-08 2.3198391E-08 1,midg,midg; igrid,midg,midg -1.1838093E-08 3.1892867E-08 gauss-seidel spectral radius is 0.9893505 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 23:12:35 rms-change max change #iterations 0.1908222 27.95908 at 10iterations 2.2627745E-02 2.804194 at 20iterations 2.7460880E-03 0.4642487 at 30iterations 3.8366808E-04 6.0565948E-02 at 40iterations 1.0320744E-04 1.7156363E-02 at 50iterations finished qdiffx linear iterations at : 23:12:38 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.0320744E-04 1.7156363E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 23:12:38 3.629u 0.216s 0:04.16 92.0% 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 23:12:38 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 = 2169 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: 2.096296 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): -11.99000 31.73200 ymin,ymax (A): -22.31400 28.52900 zmin,zma (A): -9.874001 41.07300 x,y,z range (A): 43.72200 50.84300 50.94700 scale (grids/A): 2.096296 object centre (A): 9.871000 3.107500 15.59950 number of atom coordinates read : 2169 total number of charged atoms : 2030 net assigned charge : 0.5000094 assigned positive charge : 316.5767 centred at (gu) : 96.11007 92.71792 92.81585 assigned negative charge : -316.0769 centred at (gu) : 95.96759 92.58851 91.93775 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20002 grid for indexing accessible points = 1.400000 m= 32242 mr = 56365 m= 6517 mr = 24559 m= 700 mr = 4515 m= 30 mr = 405 m= 0 mr = 8 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 34704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16116 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) : 0.6987653 object centre at (A) : 9.871000 3.107500 15.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6525798E-02 -1.8484714E-02 midg,1,midg; midg,igrid,midg 3.4019951E-02 6.4710811E-02 1,midg,midg; igrid,midg,midg -1.8341120E-02 -4.0255133E-03 gauss-seidel spectral radius is 0.9988285 estimated iterations to convergence 231 setup time was (sec) 0.9400000 now iterating at: 23:12:40 rms-change max change #iterations 4.548362 260.9354 at 10iterations 2.245930 85.19027 at 20iterations 1.114815 35.75742 at 30iterations 0.5531170 16.47893 at 40iterations 0.2728237 9.076692 at 50iterations 0.1363990 3.903186 at 60iterations 6.7400470E-02 2.192290 at 70iterations 3.3516299E-02 1.043556 at 80iterations 1.6652128E-02 0.5136986 at 90iterations 8.2918582E-03 0.2531662 at 100iterations 4.1489494E-03 0.1321204 at 110iterations 2.0961491E-03 6.7073822E-02 at 120iterations finished qdiffx linear iterations at : 23:12:46 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.0961491E-03 6.7073822E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 23:12:47 7.747u 0.194s 0:08.22 96.4% 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 Sun Oct 9 2011 at 23:12:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 3.144444 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): -11.99000 31.73200 ymin,ymax (A): -22.31400 28.52900 zmin,zma (A): -9.874001 41.07300 x,y,z range (A): 43.72200 50.84300 50.94700 scale (grids/A): 3.144444 object centre (A): 9.871000 3.107500 15.59950 number of atom coordinates read : 2169 total number of charged atoms : 2030 net assigned charge : 0.5000094 assigned positive charge : 316.5767 centred at (gu) : 99.16494 94.07685 94.22360 assigned negative charge : -316.0769 centred at (gu) : 98.95142 93.88274 92.90652 start vw surface at 0.2200000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 186940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20002 grid for indexing accessible points = 1.400000 m= 100098 mr = 135949 m= 41345 mr = 83181 m= 12478 mr = 34243 m= 2771 mr = 9955 m= 357 mr = 2158 m= 19 mr = 271 m= 0 mr = 5 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 78246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 16240 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) : 2.096296 object centre at (A) : 9.871000 3.107500 15.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6961823 -0.3332294 midg,1,midg; midg,igrid,midg 0.3080327 0.6383811 1,midg,midg; igrid,midg,midg -0.2174731 -6.5001070E-02 gauss-seidel spectral radius is 0.9993130 estimated iterations to convergence 301 setup time was (sec) 2.360000 now iterating at: 23:12:49 rms-change max change #iterations 10.31855 416.7729 at 10iterations 6.173322 136.9724 at 20iterations 3.682767 77.77432 at 30iterations 2.190319 50.35451 at 40iterations 1.296875 27.57659 at 50iterations 0.7695814 13.83997 at 60iterations 0.4555640 7.576118 at 70iterations 0.2682106 5.312927 at 80iterations 0.1583722 3.069876 at 90iterations 9.3175158E-02 1.721422 at 100iterations 5.4813460E-02 0.9089041 at 110iterations 3.2307111E-02 0.5355988 at 120iterations 1.9034687E-02 0.3208714 at 130iterations 1.1187037E-02 0.1923218 at 140iterations 6.5802215E-03 0.1119843 at 150iterations 3.8814940E-03 6.2798977E-02 at 160iterations 2.3078364E-03 4.2875290E-02 at 170iterations 1.3840288E-03 2.2929668E-02 at 180iterations finished qdiffx linear iterations at : 23:13:01 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 1.3840288E-03 2.2929668E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 23:13:01 13.866u 0.212s 0:14.35 98.0% 0+0k 0+0io 0pf+0w