Sat Oct 8 17:58:01 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 Sat Oct 8 2011 at 17:58:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 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: 0.5669331 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): -93.00700 -30.21300 ymin,ymax (A): -66.06000 -5.950000 zmin,zma (A): 10.76400 68.56300 x,y,z range (A): 62.79400 60.11000 57.79900 scale (grids/A): 0.5669331 object centre (A): -61.61000 -36.00500 39.66350 number of atom coordinates read : 3671 total number of charged atoms : 3520 net assigned charge : -5.499973 assigned positive charge : 551.2707 centred at (gu) : 90.60348 90.86173 88.35440 assigned negative charge : -556.7728 centred at (gu) : 90.65067 90.81621 88.37659 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7947 nv = 96 ne = 84 npr = 72260 no. pairs analyzed = 72260 no. exposed pairs = 4992 no. arc points = 34963 no. surface atoms = 1664 nbur = 2007 mkacc time = 0.1500000 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= 365 mr = 4030 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3527 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10170 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3375843E-10 -7.8558043E-10 midg,1,midg; midg,igrid,midg -1.2790156E-09 5.5344271E-11 1,midg,midg; igrid,midg,midg 5.2695275E-11 -1.8456603E-09 gauss-seidel spectral radius is 0.9840124 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 17:58:02 rms-change max change #iterations 9.7681358E-02 14.54460 at 10iterations 7.2606825E-03 1.048607 at 20iterations 6.6000363E-04 0.1010857 at 30iterations 1.4294290E-04 2.3959160E-02 at 40iterations 4.8054600E-05 8.4114075E-03 at 50iterations finished qdiffx linear iterations at : 17:58:04 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 4.8054600E-05 8.4114075E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 17:58:05 3.183u 0.151s 0:03.63 91.7% 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 8 2011 at 17:58:05 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 = 3671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.700799 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): -93.00700 -30.21300 ymin,ymax (A): -66.06000 -5.950000 zmin,zma (A): 10.76400 68.56300 x,y,z range (A): 62.79400 60.11000 57.79900 scale (grids/A): 1.700799 object centre (A): -61.61000 -36.00500 39.66350 number of atom coordinates read : 3671 total number of charged atoms : 3520 net assigned charge : -5.499973 assigned positive charge : 551.2707 centred at (gu) : 91.80941 92.58402 85.06207 assigned negative charge : -556.7728 centred at (gu) : 91.95163 92.44836 85.12947 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34963 grid for indexing accessible points = 1.400000 m= 28653 mr = 58389 m= 3368 mr = 19602 m= 86 mr = 1578 m= 0 mr = 7 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.6000000 number of dielectric boundary points 39535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 27268 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) : 0.5669331 object centre at (A) : -61.61000 -36.00500 39.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4441869E-03 -1.6557397E-02 midg,1,midg; midg,igrid,midg -1.5477143E-02 4.3514869E-03 1,midg,midg; igrid,midg,midg -4.2902743E-03 -1.3359931E-02 gauss-seidel spectral radius is 0.9984187 estimated iterations to convergence 200 setup time was (sec) 0.9000000 now iterating at: 17:58:06 rms-change max change #iterations 4.116917 159.4375 at 10iterations 1.803558 59.96078 at 20iterations 0.7970837 28.23101 at 30iterations 0.3516414 11.00274 at 40iterations 0.1553642 5.221138 at 50iterations 6.8780825E-02 2.102839 at 60iterations 3.0309705E-02 0.9584298 at 70iterations 1.3385232E-02 0.4136126 at 80iterations 5.9845792E-03 0.2046843 at 90iterations 2.6816702E-03 8.8976860E-02 at 100iterations 1.2250557E-03 4.1545868E-02 at 110iterations 5.7978788E-04 1.8632889E-02 at 120iterations finished qdiffx linear iterations at : 17:58:12 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 5.7978788E-04 1.8632889E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 17:58:13 7.610u 0.235s 0:08.14 96.3% 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 8 2011 at 17:58:13 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 = 3671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.551199 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): -93.00700 -30.21300 ymin,ymax (A): -66.06000 -5.950000 zmin,zma (A): 10.76400 68.56300 x,y,z range (A): 62.79400 60.11000 57.79900 scale (grids/A): 2.551199 object centre (A): -61.61000 -36.00500 39.66350 number of atom coordinates read : 3671 total number of charged atoms : 3520 net assigned charge : -5.499973 assigned positive charge : 551.2707 centred at (gu) : 92.71387 93.87573 82.59278 assigned negative charge : -556.7728 centred at (gu) : 92.92730 93.67246 82.69412 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 201389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34963 grid for indexing accessible points = 1.400000 m= 96824 mr = 142605 m= 29521 mr = 76279 m= 5454 mr = 21868 m= 428 mr = 3520 m= 7 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 1.470000 number of dielectric boundary points 89185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 28152 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) : 1.700799 object centre at (A) : -61.61000 -36.00500 39.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2027702 -0.2527766 midg,1,midg; midg,igrid,midg -0.1564431 3.8764294E-02 1,midg,midg; igrid,midg,midg -4.6807814E-02 -0.2991870 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.800000 now iterating at: 17:58:15 rms-change max change #iterations 10.56143 297.2468 at 10iterations 6.220572 140.4941 at 20iterations 3.638413 79.81894 at 30iterations 2.117820 47.14339 at 40iterations 1.224819 27.29158 at 50iterations 0.7082248 13.16647 at 60iterations 0.4066682 7.849957 at 70iterations 0.2333681 4.455832 at 80iterations 0.1335752 2.575758 at 90iterations 7.6552115E-02 1.325758 at 100iterations 4.3694612E-02 0.8148651 at 110iterations 2.5011308E-02 0.4680672 at 120iterations 1.4278708E-02 0.2486439 at 130iterations 8.1605474E-03 0.1391993 at 140iterations 4.6566539E-03 8.5677147E-02 at 150iterations 2.6698380E-03 4.9962997E-02 at 160iterations 1.5363063E-03 2.7030945E-02 at 170iterations 8.8972121E-04 1.4662027E-02 at 180iterations finished qdiffx linear iterations at : 17:58:26 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 8.8972121E-04 1.4662027E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 17:58:26 12.746u 0.220s 0:13.28 97.5% 0+0k 0+0io 0pf+0w