Mon Oct 10 19:35:03 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 Mon Oct 10 2011 at 19:35:03 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2691 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5597220 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): -8.143001 38.01800 ymin,ymax (A): -9.147000 41.70600 zmin,zma (A): -1.282000 62.32100 x,y,z range (A): 46.16100 50.85300 63.60300 scale (grids/A): 0.5597220 object centre (A): 14.93750 16.27950 30.51950 number of atom coordinates read : 2691 total number of charged atoms : 2546 net assigned charge : 2.806024 assigned positive charge : 398.1158 centred at (gu) : 90.68453 89.27772 89.29255 assigned negative charge : -395.3106 centred at (gu) : 90.60188 89.21811 89.39249 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5572 nv = 96 ne = 84 npr = 53632 no. pairs analyzed = 53632 no. exposed pairs = 3549 no. arc points = 24720 no. surface atoms = 1195 nbur = 1496 mkacc time = 0.1200000 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 = 1.540000 m= 231 mr = 2806 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2494 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4850188E-09 -5.8599292E-10 midg,1,midg; midg,igrid,midg -3.6000164E-10 7.2561918E-10 1,midg,midg; igrid,midg,midg -4.4357854E-10 1.2814684E-09 gauss-seidel spectral radius is 0.9835160 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 19:35:04 rms-change max change #iterations 7.7982299E-02 13.99137 at 10iterations 5.4521919E-03 0.8838158 at 20iterations 3.9441907E-04 6.1584473E-02 at 30iterations 2.8099121E-05 4.5433044E-03 at 40iterations 2.1412000E-06 3.3807755E-04 at 50iterations finished qdiffx linear iterations at : 19:35:07 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.1412000E-06 3.3807755E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 19:35:07 3.374u 0.201s 0:03.94 90.6% 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 19:35:07 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2691 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.679166 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): -8.143001 38.01800 ymin,ymax (A): -9.147000 41.70600 zmin,zma (A): -1.282000 62.32100 x,y,z range (A): 46.16100 50.85300 63.60300 scale (grids/A): 1.679166 object centre (A): 14.93750 16.27950 30.51950 number of atom coordinates read : 2691 total number of charged atoms : 2546 net assigned charge : 2.806024 assigned positive charge : 398.1158 centred at (gu) : 92.05334 87.83268 87.87724 assigned negative charge : -395.3106 centred at (gu) : 91.80554 87.65424 88.17725 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24720 grid for indexing accessible points = 1.400000 m= 19369 mr = 40702 m= 2200 mr = 13294 m= 73 mr = 1116 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 413 time to turn everything in is 0.4500000 number of dielectric boundary points 27676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 245 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 19639 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) : 0.5597220 object centre at (A) : 14.93750 16.27950 30.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2037083E-02 1.1166863E-02 midg,1,midg; midg,igrid,midg -9.5211249E-03 -2.4850473E-03 1,midg,midg; igrid,midg,midg -1.9730097E-03 2.7171618E-03 gauss-seidel spectral radius is 0.9982611 estimated iterations to convergence 190 setup time was (sec) 0.7300000 now iterating at: 19:35:08 rms-change max change #iterations 3.328739 166.2827 at 10iterations 1.403223 55.87339 at 20iterations 0.5949168 21.93662 at 30iterations 0.2521311 9.293188 at 40iterations 0.1065538 3.845066 at 50iterations 4.5502238E-02 1.624798 at 60iterations 1.9296069E-02 0.7197361 at 70iterations 8.1894854E-03 0.2876148 at 80iterations 3.4753596E-03 0.1325178 at 90iterations 1.4781596E-03 5.4206848E-02 at 100iterations 6.2709011E-04 2.2735596E-02 at 110iterations 2.6732788E-04 9.1552734E-03 at 120iterations finished qdiffx linear iterations at : 19:35:15 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 2.6732788E-04 9.1552734E-03 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 19:35:15 7.375u 0.199s 0:07.99 94.6% 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 19:35:15 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2691 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.518749 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): -8.143001 38.01800 ymin,ymax (A): -9.147000 41.70600 zmin,zma (A): -1.282000 62.32100 x,y,z range (A): 46.16100 50.85300 63.60300 scale (grids/A): 2.518749 object centre (A): 14.93750 16.27950 30.51950 number of atom coordinates read : 2691 total number of charged atoms : 2546 net assigned charge : 2.806024 assigned positive charge : 398.1158 centred at (gu) : 93.07967 86.74891 86.81569 assigned negative charge : -395.3106 centred at (gu) : 92.70826 86.48135 87.26584 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 141757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24720 grid for indexing accessible points = 1.400000 m= 65811 mr = 99550 m= 19936 mr = 51820 m= 3663 mr = 15067 m= 319 mr = 2408 m= 6 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 1.040000 number of dielectric boundary points 62498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20355 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) : 1.679166 object centre at (A) : 14.93750 16.27950 30.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3810422 0.3181947 midg,1,midg; midg,igrid,midg -8.4931366E-02 -5.3179625E-02 1,midg,midg; igrid,midg,midg -3.4615126E-02 2.8003750E-02 gauss-seidel spectral radius is 0.9991612 estimated iterations to convergence 273 setup time was (sec) 1.340000 now iterating at: 19:35:17 rms-change max change #iterations 8.532470 353.9089 at 10iterations 4.815279 136.9421 at 20iterations 2.700917 90.65698 at 30iterations 1.512174 35.43680 at 40iterations 0.8421170 20.66938 at 50iterations 0.4693334 10.97504 at 60iterations 0.2609973 7.402860 at 70iterations 0.1447576 3.017971 at 80iterations 8.0133960E-02 1.696598 at 90iterations 4.4397179E-02 1.007172 at 100iterations 2.4632744E-02 0.5232124 at 110iterations 1.3624140E-02 0.2702293 at 120iterations 7.5379517E-03 0.1522635 at 130iterations 4.1716425E-03 9.0742588E-02 at 140iterations 2.3099086E-03 4.7840118E-02 at 150iterations 1.2785642E-03 2.6674032E-02 at 160iterations 7.0691254E-04 1.5731812E-02 at 170iterations 3.9170490E-04 8.8787079E-03 at 180iterations finished qdiffx linear iterations at : 19:35:27 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 3.9170490E-04 8.8787079E-03 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 19:35:28 11.768u 0.224s 0:12.32 97.2% 0+0k 0+0io 0pf+0w