Sun Oct 9 08:46:25 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 Sun Oct 9 2011 at 08:46:25 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5330 !!! WARNING: HIR 740 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4910684 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): 27.75000 95.67700 ymin,ymax (A): 21.84200 86.46000 zmin,zma (A): 45.41400 117.9090 x,y,z range (A): 67.92700 64.61800 72.49500 scale (grids/A): 0.4910684 object centre (A): 61.71350 54.15100 81.66150 number of atom coordinates read : 5330 total number of charged atoms : 5168 net assigned charge : 4.014040 assigned positive charge : 801.7910 centred at (gu) : 90.17790 88.71714 90.51802 assigned negative charge : -797.7830 centred at (gu) : 90.13035 88.77828 90.66078 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8197 nv = 96 ne = 84 npr = 105250 no. pairs analyzed = 105250 no. exposed pairs = 6839 no. arc points = 47725 no. surface atoms = 2295 nbur = 3035 mkacc time = 0.2300000 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 = 1.736000 m= 302 mr = 4091 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4602 ## 715 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10994 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6730026E-10 -1.7789542E-10 midg,1,midg; midg,igrid,midg 1.3772300E-10 -3.6215708E-11 1,midg,midg; igrid,midg,midg -3.3422938E-11 8.4336163E-11 gauss-seidel spectral radius is 0.9788494 estimated iterations to convergence 57 setup time was (sec) 0.7000000 now iterating at: 08:46:26 rms-change max change #iterations 5.8815338E-02 9.921173 at 10iterations 3.5350872E-03 0.6002121 at 20iterations 6.3230400E-04 0.1710815 at 30iterations 1.9592702E-04 5.2444458E-02 at 40iterations 6.4534164E-05 1.6624451E-02 at 50iterations finished qdiffx linear iterations at : 08:46:28 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 6.4534164E-05 1.6624451E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:46:29 3.377u 0.171s 0:03.83 92.4% 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 08:46:29 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5330 !!! WARNING: HIR 740 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.473205 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): 27.75000 95.67700 ymin,ymax (A): 21.84200 86.46000 zmin,zma (A): 45.41400 117.9090 x,y,z range (A): 67.92700 64.61800 72.49500 scale (grids/A): 1.473205 object centre (A): 61.71350 54.15100 81.66150 number of atom coordinates read : 5330 total number of charged atoms : 5168 net assigned charge : 4.014040 assigned positive charge : 801.7910 centred at (gu) : 90.53223 86.14990 91.55261 assigned negative charge : -797.7830 centred at (gu) : 90.39050 86.33463 91.98225 start vw surface at 0.2500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 92428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47725 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26036 mr = 62023 m= 1928 mr = 16811 m= 34 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 0.7200000 number of dielectric boundary points 40873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 714 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 38239 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) : 0.4910684 object centre at (A) : 61.71350 54.15100 81.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6553098E-02 -4.4071148E-03 midg,1,midg; midg,igrid,midg -6.8552268E-04 -9.3438867E-03 1,midg,midg; igrid,midg,midg 8.4036579E-03 1.8981352E-02 gauss-seidel spectral radius is 0.9980047 estimated iterations to convergence 178 setup time was (sec) 1.010000 now iterating at: 08:46:30 rms-change max change #iterations 3.677689 159.5406 at 10iterations 1.463032 50.65506 at 20iterations 0.5866096 20.43534 at 30iterations 0.2346905 7.885679 at 40iterations 9.3985550E-02 3.018362 at 50iterations 3.7630972E-02 1.266775 at 60iterations 1.5077754E-02 0.5407219 at 70iterations 6.1528268E-03 0.1929932 at 80iterations 2.5330049E-03 8.0413818E-02 at 90iterations 1.0813997E-03 3.9649963E-02 at 100iterations 5.0085475E-04 2.2882462E-02 at 110iterations 2.5920186E-04 1.1739731E-02 at 120iterations finished qdiffx linear iterations at : 08:46:37 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 2.5920186E-04 1.1739731E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 08:46:37 7.660u 0.182s 0:08.13 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 08:46:37 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5330 !!! WARNING: HIR 740 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.209808 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): 27.75000 95.67700 ymin,ymax (A): 21.84200 86.46000 zmin,zma (A): 45.41400 117.9090 x,y,z range (A): 67.92700 64.61800 72.49500 scale (grids/A): 2.209808 object centre (A): 61.71350 54.15100 81.66150 number of atom coordinates read : 5330 total number of charged atoms : 5168 net assigned charge : 4.014040 assigned positive charge : 801.7910 centred at (gu) : 90.79806 84.22446 92.32852 assigned negative charge : -797.7830 centred at (gu) : 90.58566 84.50197 92.97337 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 215428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47725 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 94062 mr = 152611 m= 22341 mr = 72328 m= 2554 mr = 15712 m= 80 mr = 1421 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 2809 time to turn everything in is 1.520000 number of dielectric boundary points 92383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 41157 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) : 1.473205 object centre at (A) : 61.71350 54.15100 81.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2794919 7.6549061E-02 midg,1,midg; midg,igrid,midg 8.4252879E-03 -0.2221784 1,midg,midg; igrid,midg,midg 0.1321298 0.3923981 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.840000 now iterating at: 08:46:39 rms-change max change #iterations 10.40041 317.4983 at 10iterations 5.968657 140.8451 at 20iterations 3.410457 72.72883 at 30iterations 1.938680 41.96888 at 40iterations 1.094367 24.68541 at 50iterations 0.6156252 13.59731 at 60iterations 0.3462207 6.965020 at 70iterations 0.1934878 4.238173 at 80iterations 0.1083407 2.040966 at 90iterations 6.0384154E-02 1.213184 at 100iterations 3.3659574E-02 0.7350826 at 110iterations 1.8740980E-02 0.3571415 at 120iterations 1.0451086E-02 0.1946540 at 130iterations 5.8056717E-03 0.1325951 at 140iterations 3.2388959E-03 5.9916019E-02 at 150iterations 1.8117512E-03 3.6033630E-02 at 160iterations 1.0164288E-03 2.1888733E-02 at 170iterations 5.7412946E-04 1.0311127E-02 at 180iterations finished qdiffx linear iterations at : 08:46:52 total time elapsed so far: 14.88000 # loops : 180 mean,max change (kT/e) : 5.7412946E-04 1.0311127E-02 energy calculations done at 14.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.06000 DelPhi exited at 08:46:53 15.057u 0.194s 0:15.53 98.1% 0+0k 0+0io 0pf+0w