Sun Oct 9 12:26:07 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 12:26:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 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: 0.6891478 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): -14.22100 37.43700 ymin,ymax (A): -0.3520000 44.83800 zmin,zma (A): -7.024000 44.25400 x,y,z range (A): 51.65800 45.19000 51.27800 scale (grids/A): 0.6891478 object centre (A): 11.60800 22.24300 18.61500 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 372.5330 centred at (gu) : 91.08527 91.28493 90.01878 assigned negative charge : -368.0336 centred at (gu) : 91.25019 91.37781 89.98048 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7711 nv = 96 ne = 84 npr = 48697 no. pairs analyzed = 48697 no. exposed pairs = 3088 no. arc points = 21462 no. surface atoms = 1034 nbur = 1399 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 492 mr = 4223 m= 0 mr = 70 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2041 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0917460E-08 4.0394458E-08 midg,1,midg; midg,igrid,midg 4.7169522E-08 -1.3785671E-08 1,midg,midg; igrid,midg,midg 7.0591625E-08 -4.8525397E-08 gauss-seidel spectral radius is 0.9890647 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 12:26:08 rms-change max change #iterations 0.1945272 27.54568 at 10iterations 2.2803647E-02 3.082363 at 20iterations 3.0683109E-03 0.5150146 at 30iterations 6.0080283E-04 8.7268829E-02 at 40iterations 1.8260028E-04 2.7631760E-02 at 50iterations finished qdiffx linear iterations at : 12:26:10 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.8260028E-04 2.7631760E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 12:26:11 3.436u 0.222s 0:03.97 91.9% 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 Sun Oct 9 2011 at 12:26:11 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 = 2433 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: 2.067444 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): -14.22100 37.43700 ymin,ymax (A): -0.3520000 44.83800 zmin,zma (A): -7.024000 44.25400 x,y,z range (A): 51.65800 45.19000 51.27800 scale (grids/A): 2.067444 object centre (A): 11.60800 22.24300 18.61500 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 372.5330 centred at (gu) : 93.25536 93.85446 90.05576 assigned negative charge : -368.0336 centred at (gu) : 93.75042 94.13314 89.94125 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21462 grid for indexing accessible points = 1.400000 m= 31851 mr = 56470 m= 5995 mr = 23718 m= 549 mr = 3940 m= 10 mr = 246 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 35735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18148 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) : 0.6891478 object centre at (A) : 11.60800 22.24300 18.61500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8053479E-02 9.8681739E-03 midg,1,midg; midg,igrid,midg 4.0383317E-02 4.6383487E-03 1,midg,midg; igrid,midg,midg 2.2921076E-02 -4.4262230E-02 gauss-seidel spectral radius is 0.9988172 estimated iterations to convergence 230 setup time was (sec) 0.9000000 now iterating at: 12:26:12 rms-change max change #iterations 4.872499 231.5732 at 10iterations 2.389216 80.15962 at 20iterations 1.183346 35.50916 at 30iterations 0.5842211 18.49350 at 40iterations 0.2883230 8.524284 at 50iterations 0.1426740 4.176789 at 60iterations 7.1050994E-02 2.334535 at 70iterations 3.4899052E-02 1.087350 at 80iterations 1.7314324E-02 0.4856987 at 90iterations 8.6978162E-03 0.2715702 at 100iterations 4.4136602E-03 0.1259518 at 110iterations 2.3022047E-03 7.1490288E-02 at 120iterations finished qdiffx linear iterations at : 12:26:19 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.3022047E-03 7.1490288E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 12:26:20 7.914u 0.268s 0:08.55 95.5% 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 12:26:20 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 = 2433 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: 3.101165 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): -14.22100 37.43700 ymin,ymax (A): -0.3520000 44.83800 zmin,zma (A): -7.024000 44.25400 x,y,z range (A): 51.65800 45.19000 51.27800 scale (grids/A): 3.101165 object centre (A): 11.60800 22.24300 18.61500 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 372.5330 centred at (gu) : 94.88289 95.78171 90.08350 assigned negative charge : -368.0336 centred at (gu) : 95.62562 96.19975 89.91188 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 188241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21462 grid for indexing accessible points = 1.400000 m= 99819 mr = 136565 m= 39933 mr = 81821 m= 11291 mr = 32444 m= 2168 mr = 8569 m= 228 mr = 1561 m= 6 mr = 132 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 80593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 18328 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) : 2.067444 object centre at (A) : 11.60800 22.24300 18.61500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2626809 -0.1738281 midg,1,midg; midg,igrid,midg 0.3462927 -6.8258047E-02 1,midg,midg; igrid,midg,midg 0.3930697 -0.5074484 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 2.240000 now iterating at: 12:26:22 rms-change max change #iterations 11.03681 511.3967 at 10iterations 6.559105 150.4129 at 20iterations 3.877253 73.84254 at 30iterations 2.285999 41.29691 at 40iterations 1.348945 24.82510 at 50iterations 0.7920531 13.64242 at 60iterations 0.4649391 8.588172 at 70iterations 0.2719378 4.425076 at 80iterations 0.1596947 3.237801 at 90iterations 9.3498118E-02 1.461857 at 100iterations 5.5044767E-02 0.9608688 at 110iterations 3.2318596E-02 0.5652618 at 120iterations 1.9145027E-02 0.3403083 at 130iterations 1.1476759E-02 0.2184296 at 140iterations 7.0290966E-03 0.1290226 at 150iterations 4.4878856E-03 9.0316772E-02 at 160iterations 3.0096616E-03 6.7138672E-02 at 170iterations 2.1549896E-03 4.7401428E-02 at 180iterations finished qdiffx linear iterations at : 12:26:33 total time elapsed so far: 13.42000 # loops : 180 mean,max change (kT/e) : 2.1549896E-03 4.7401428E-02 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 12:26:34 13.602u 0.274s 0:14.18 97.8% 0+0k 0+0io 0pf+0w