Sat Oct 15 15:27:50 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 Sat Oct 15 2011 at 15:27:50 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 77 has a net charge of -0.1880 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: ZN8 849 has a net charge of 1.4000 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: 0.6171983 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): 101.8300 159.1170 ymin,ymax (A): 54.85600 107.9080 zmin,zma (A): -58.23500 -0.5549999 x,y,z range (A): 57.28700 53.05201 57.68000 scale (grids/A): 0.6171983 object centre (A): 130.4735 81.38200 -29.39500 number of atom coordinates read : 2990 total number of charged atoms : 2819 net assigned charge : 6.363020 assigned positive charge : 457.9874 centred at (gu) : 90.85814 89.57652 90.37421 assigned negative charge : -451.6250 centred at (gu) : 91.04501 89.74315 90.53742 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 60044 no. pairs analyzed = 60044 no. exposed pairs = 3700 no. arc points = 25873 no. surface atoms = 1248 nbur = 1742 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 4149 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2552 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9262 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4972040E-08 -7.6271744E-09 midg,1,midg; midg,igrid,midg 1.8130535E-08 -6.5584604E-09 1,midg,midg; igrid,midg,midg 1.4794710E-08 -1.0678433E-08 gauss-seidel spectral radius is 0.9864382 estimated iterations to convergence 70 setup time was (sec) 0.7000000 now iterating at: 15:27:51 rms-change max change #iterations 0.1368725 19.57783 at 10iterations 1.2588288E-02 1.886204 at 20iterations 1.1932916E-03 0.1979294 at 30iterations 1.5919893E-04 2.3582458E-02 at 40iterations 4.4943619E-05 6.8511963E-03 at 50iterations finished qdiffx linear iterations at : 15:27:55 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 4.4943619E-05 6.8511963E-03 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.360000 DelPhi exited at 15:27:57 5.367u 0.482s 0:07.59 76.9% 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 Sat Oct 15 2011 at 15:27:57 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 77 has a net charge of -0.1880 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: ZN8 849 has a net charge of 1.4000 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: 1.851595 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): 101.8300 159.1170 ymin,ymax (A): 54.85600 107.9080 zmin,zma (A): -58.23500 -0.5549999 x,y,z range (A): 57.28700 53.05201 57.68000 scale (grids/A): 1.851595 object centre (A): 130.4735 81.38200 -29.39500 number of atom coordinates read : 2990 total number of charged atoms : 2819 net assigned charge : 6.363020 assigned positive charge : 457.9874 centred at (gu) : 92.57383 88.72897 91.12215 assigned negative charge : -451.6250 centred at (gu) : 93.13457 89.22873 91.61192 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25873 grid for indexing accessible points = 1.400000 m= 28221 mr = 56415 m= 3960 mr = 20645 m= 162 mr = 2316 m= 0 mr = 27 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2040 time to turn everything in is 0.6900000 number of dielectric boundary points 34275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22090 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) : 0.6171983 object centre at (A) : 130.4735 81.38200 -29.39500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4072831E-02 -8.0116522E-03 midg,1,midg; midg,igrid,midg -8.6222896E-03 -1.7458029E-02 1,midg,midg; igrid,midg,midg 6.6839688E-02 -6.7829052E-03 gauss-seidel spectral radius is 0.9986007 estimated iterations to convergence 212 setup time was (sec) 1.110000 now iterating at: 15:28:03 rms-change max change #iterations 4.417972 166.9589 at 10iterations 2.045415 69.06173 at 20iterations 0.9528124 33.30017 at 30iterations 0.4416666 14.70829 at 40iterations 0.2061383 6.871243 at 50iterations 9.5447488E-02 2.971278 at 60iterations 4.4430729E-02 1.364571 at 70iterations 2.0629555E-02 0.6683731 at 80iterations 9.5980018E-03 0.3037109 at 90iterations 4.4700070E-03 0.1348572 at 100iterations 2.0853013E-03 6.4167023E-02 at 110iterations 9.7635604E-04 3.0863643E-02 at 120iterations finished qdiffx linear iterations at : 15:28:15 total time elapsed so far: 12.88000 # loops : 120 mean,max change (kT/e) : 9.7635604E-04 3.0863643E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 15:28:16 13.069u 0.520s 0:18.57 73.1% 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 Sat Oct 15 2011 at 15:28:16 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: 371 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 77 has a net charge of -0.1880 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: ZN8 849 has a net charge of 1.4000 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: 2.777392 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): 101.8300 159.1170 ymin,ymax (A): 54.85600 107.9080 zmin,zma (A): -58.23500 -0.5549999 x,y,z range (A): 57.28700 53.05201 57.68000 scale (grids/A): 2.777392 object centre (A): 130.4735 81.38200 -29.39500 number of atom coordinates read : 2990 total number of charged atoms : 2819 net assigned charge : 6.363020 assigned positive charge : 457.9874 centred at (gu) : 93.86053 88.09332 91.68309 assigned negative charge : -451.6250 centred at (gu) : 94.70168 88.84299 92.41779 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 188394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25873 grid for indexing accessible points = 1.400000 m= 93280 mr = 137199 m= 31509 mr = 75946 m= 6858 mr = 24928 m= 793 mr = 4962 m= 32 mr = 464 m= 0 mr = 12 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 6672 time to turn everything in is 1.810000 number of dielectric boundary points 77355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 22550 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) : 1.851595 object centre at (A) : 130.4735 81.38200 -29.39500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5374435 3.7400603E-02 midg,1,midg; midg,igrid,midg -0.2243593 -0.1512613 1,midg,midg; igrid,midg,midg 0.9009112 -0.1325426 gauss-seidel spectral radius is 0.9992546 estimated iterations to convergence 289 setup time was (sec) 2.180000 now iterating at: 15:28:22 rms-change max change #iterations 10.49281 381.7432 at 10iterations 6.180873 127.9902 at 20iterations 3.603123 75.40612 at 30iterations 2.098189 39.72446 at 40iterations 1.215658 23.33224 at 50iterations 0.7039439 15.45525 at 60iterations 0.4079107 7.503231 at 70iterations 0.2356717 4.164866 at 80iterations 0.1357942 2.439268 at 90iterations 7.8331567E-02 1.391144 at 100iterations 4.5088872E-02 0.7838650 at 110iterations 2.5902804E-02 0.4567537 at 120iterations 1.4912087E-02 0.2680740 at 130iterations 8.5815666E-03 0.1521025 at 140iterations 4.9378257E-03 8.8268280E-02 at 150iterations 2.8403858E-03 4.9819946E-02 at 160iterations 1.6354332E-03 2.9586792E-02 at 170iterations 9.4389205E-04 1.6975403E-02 at 180iterations finished qdiffx linear iterations at : 15:28:48 total time elapsed so far: 23.55000 # loops : 180 mean,max change (kT/e) : 9.4389205E-04 1.6975403E-02 energy calculations done at 23.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.72000 DelPhi exited at 15:28:49 23.725u 0.545s 0:32.40 74.8% 0+0k 0+0io 0pf+0w