Mon Oct 10 14:06:28 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 Mon Oct 10 2011 at 14:06:29 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 = 3380 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: 0.5358460 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): -15.03200 41.48700 ymin,ymax (A): -39.44500 26.99200 zmin,zma (A): -17.46700 35.12700 x,y,z range (A): 56.51900 66.43700 52.59400 scale (grids/A): 0.5358460 object centre (A): 13.22750 -6.226501 8.830002 number of atom coordinates read : 3380 total number of charged atoms : 3236 net assigned charge : -0.9999895 assigned positive charge : 505.8435 centred at (gu) : 91.20860 91.92498 90.66027 assigned negative charge : -506.8448 centred at (gu) : 91.16317 91.87512 90.61779 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6231 nv = 96 ne = 84 npr = 69006 no. pairs analyzed = 69006 no. exposed pairs = 4115 no. arc points = 28450 no. surface atoms = 1398 nbur = 1982 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 = 1.596000 m= 251 mr = 3329 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8248 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2839575E-10 1.9557855E-10 midg,1,midg; midg,igrid,midg -1.8982735E-10 3.3422212E-10 1,midg,midg; igrid,midg,midg -2.1017796E-10 2.4613628E-10 gauss-seidel spectral radius is 0.9820766 estimated iterations to convergence 62 setup time was (sec) 0.5900000 now iterating at: 14:06:29 rms-change max change #iterations 6.8419069E-02 11.50297 at 10iterations 4.5505017E-03 0.6704373 at 20iterations 3.5565524E-04 6.2091827E-02 at 30iterations 5.7093195E-05 1.0424614E-02 at 40iterations 1.3250924E-05 2.5348663E-03 at 50iterations finished qdiffx linear iterations at : 14:06:32 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.3250924E-05 2.5348663E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:06:32 3.440u 0.171s 0:03.98 90.7% 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 Mon Oct 10 2011 at 14:06:33 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 = 3380 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: 1.607538 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): -15.03200 41.48700 ymin,ymax (A): -39.44500 26.99200 zmin,zma (A): -17.46700 35.12700 x,y,z range (A): 56.51900 66.43700 52.59400 scale (grids/A): 1.607538 object centre (A): 13.22750 -6.226501 8.830002 number of atom coordinates read : 3380 total number of charged atoms : 3236 net assigned charge : -0.9999895 assigned positive charge : 505.8435 centred at (gu) : 93.62485 95.77418 91.97974 assigned negative charge : -506.8448 centred at (gu) : 93.48911 95.62505 91.85307 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21970 mr = 48625 m= 2076 mr = 15360 m= 59 mr = 866 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 364 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 24693 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) : 0.5358460 object centre at (A) : 13.22750 -6.226501 8.830002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3765533E-03 5.5995784E-03 midg,1,midg; midg,igrid,midg 4.3172599E-03 1.1631096E-02 1,midg,midg; igrid,midg,midg -4.2705662E-03 -2.9058070E-03 gauss-seidel spectral radius is 0.9981543 estimated iterations to convergence 185 setup time was (sec) 0.7900000 now iterating at: 14:06:34 rms-change max change #iterations 3.401174 172.8767 at 10iterations 1.408258 63.55271 at 20iterations 0.5835191 22.37598 at 30iterations 0.2418806 9.092531 at 40iterations 9.9985965E-02 3.488262 at 50iterations 4.1665118E-02 1.554493 at 60iterations 1.7271902E-02 0.6773996 at 70iterations 7.1735536E-03 0.2455825 at 80iterations 2.9802206E-03 0.1029282 at 90iterations 1.2413027E-03 4.6429634E-02 at 100iterations 5.1960157E-04 1.7135382E-02 at 110iterations 2.2004345E-04 7.4958801E-03 at 120iterations finished qdiffx linear iterations at : 14:06:40 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 2.2004345E-04 7.4958801E-03 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 14:06:41 7.479u 0.224s 0:08.44 91.1% 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 14:06:41 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 = 3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.411307 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): -15.03200 41.48700 ymin,ymax (A): -39.44500 26.99200 zmin,zma (A): -17.46700 35.12700 x,y,z range (A): 56.51900 66.43700 52.59400 scale (grids/A): 2.411307 object centre (A): 13.22750 -6.226501 8.830002 number of atom coordinates read : 3380 total number of charged atoms : 3236 net assigned charge : -0.9999895 assigned positive charge : 505.8435 centred at (gu) : 95.43714 98.66089 92.96922 assigned negative charge : -506.8448 centred at (gu) : 95.23358 98.43745 92.77962 start vw surface at 0.1800000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76972 mr = 119197 m= 21345 mr = 61418 m= 3087 mr = 15909 m= 193 mr = 1807 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 65611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 25849 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) : 1.607538 object centre at (A) : 13.22750 -6.226501 8.830002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1175690 8.9428432E-02 midg,1,midg; midg,igrid,midg 9.4454652E-03 0.3825378 1,midg,midg; igrid,midg,midg -3.8755082E-02 -4.0026028E-02 gauss-seidel spectral radius is 0.9991317 estimated iterations to convergence 268 setup time was (sec) 1.530000 now iterating at: 14:06:43 rms-change max change #iterations 8.948925 283.8625 at 10iterations 5.013282 127.7322 at 20iterations 2.799339 70.24012 at 30iterations 1.552960 33.90449 at 40iterations 0.8607725 19.81582 at 50iterations 0.4754943 10.00267 at 60iterations 0.2621942 5.342175 at 70iterations 0.1442884 2.902561 at 80iterations 7.9593860E-02 1.549904 at 90iterations 4.3779034E-02 0.8502769 at 100iterations 2.4054434E-02 0.4885254 at 110iterations 1.3226438E-02 0.2643285 at 120iterations 7.2675440E-03 0.1444931 at 130iterations 3.9976109E-03 7.3816299E-02 at 140iterations 2.2032973E-03 4.1732788E-02 at 150iterations 1.2079092E-03 2.3192644E-02 at 160iterations 6.6744856E-04 1.3561249E-02 at 170iterations 3.7159724E-04 7.7810287E-03 at 180iterations finished qdiffx linear iterations at : 14:06:53 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 3.7159724E-04 7.7810287E-03 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 14:06:54 12.106u 0.225s 0:12.67 97.2% 0+0k 0+0io 0pf+0w