Mon Oct 10 10:42:36 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 Mon Oct 10 2011 at 10:42:36 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5267 !!! WARNING: HIR 706 has a net charge of 0.5140 !!! WARNING: ADP 1560 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5299512 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): -10.17400 57.00200 ymin,ymax (A): -49.59200 12.48400 zmin,zma (A): -19.38700 46.32300 x,y,z range (A): 67.17600 62.07600 65.71000 scale (grids/A): 0.5299512 object centre (A): 23.41400 -18.55400 13.46800 number of atom coordinates read : 5267 total number of charged atoms : 5112 net assigned charge : 9.014014 assigned positive charge : 837.3336 centred at (gu) : 89.10312 90.88858 88.95468 assigned negative charge : -828.3268 centred at (gu) : 89.08130 90.94247 89.01904 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9616 nv = 96 ne = 84 npr = 104033 no. pairs analyzed = 104033 no. exposed pairs = 6409 no. arc points = 43209 no. surface atoms = 2143 nbur = 3124 mkacc time = 0.2700000 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 = 1.624000 m= 348 mr = 5372 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.5500000 number of dielectric boundary points 4582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4369 ## 585 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3831054E-10 -1.0321324E-10 midg,1,midg; midg,igrid,midg 5.1938198E-10 -8.9527039E-11 1,midg,midg; igrid,midg,midg 1.8261047E-10 3.5038991E-10 gauss-seidel spectral radius is 0.9818180 estimated iterations to convergence 61 setup time was (sec) 0.8200000 now iterating at: 10:42:37 rms-change max change #iterations 8.8039786E-02 11.24106 at 10iterations 5.6470465E-03 0.8720741 at 20iterations 6.9463544E-04 9.4093323E-02 at 30iterations 3.0803282E-04 4.4326782E-02 at 40iterations 1.6390433E-04 2.3461819E-02 at 50iterations finished qdiffx linear iterations at : 10:42:41 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 1.6390433E-04 2.3461819E-02 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 10:42:42 4.867u 0.379s 0:05.50 95.0% 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 10:42:42 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5267 !!! WARNING: HIR 706 has a net charge of 0.5140 !!! WARNING: ADP 1560 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.589853 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): -10.17400 57.00200 ymin,ymax (A): -49.59200 12.48400 zmin,zma (A): -19.38700 46.32300 x,y,z range (A): 67.17600 62.07600 65.71000 scale (grids/A): 1.589853 object centre (A): 23.41400 -18.55400 13.46800 number of atom coordinates read : 5267 total number of charged atoms : 5112 net assigned charge : 9.014014 assigned positive charge : 837.3336 centred at (gu) : 87.30759 92.66431 86.86256 assigned negative charge : -828.3268 centred at (gu) : 87.24402 92.82732 87.05699 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 108734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43209 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34395 mr = 77906 m= 3280 mr = 24257 m= 60 mr = 1526 m= 0 mr = 7 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2917 time to turn everything in is 0.8600000 number of dielectric boundary points 42773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 542 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 38788 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) : 0.5299512 object centre at (A) : 23.41400 -18.55400 13.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2195072E-03 -4.8695102E-02 midg,1,midg; midg,igrid,midg 1.0625850E-02 3.1737033E-03 1,midg,midg; igrid,midg,midg 4.1703735E-03 3.0065142E-02 gauss-seidel spectral radius is 0.9983004 estimated iterations to convergence 193 setup time was (sec) 1.170000 now iterating at: 10:42:43 rms-change max change #iterations 4.502311 189.2219 at 10iterations 1.929443 58.54195 at 20iterations 0.8296126 24.14971 at 30iterations 0.3569202 10.51640 at 40iterations 0.1536003 4.084660 at 50iterations 6.5812550E-02 1.994019 at 60iterations 2.8417123E-02 0.8354053 at 70iterations 1.2287530E-02 0.3760834 at 80iterations 5.3237248E-03 0.1533203 at 90iterations 2.3395373E-03 7.1116447E-02 at 100iterations 1.0730955E-03 3.9016724E-02 at 110iterations 5.4522260E-04 1.8918037E-02 at 120iterations finished qdiffx linear iterations at : 10:42:54 total time elapsed so far: 11.97000 # loops : 120 mean,max change (kT/e) : 5.4522260E-04 1.8918037E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 10:42:54 12.144u 0.457s 0:12.86 97.9% 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 Mon Oct 10 2011 at 10:42:55 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5267 !!! WARNING: HIR 706 has a net charge of 0.5140 !!! WARNING: ADP 1560 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.384780 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): -10.17400 57.00200 ymin,ymax (A): -49.59200 12.48400 zmin,zma (A): -19.38700 46.32300 x,y,z range (A): 67.17600 62.07600 65.71000 scale (grids/A): 2.384780 object centre (A): 23.41400 -18.55400 13.46800 number of atom coordinates read : 5267 total number of charged atoms : 5112 net assigned charge : 9.014014 assigned positive charge : 837.3336 centred at (gu) : 85.96091 93.99620 85.29346 assigned negative charge : -828.3268 centred at (gu) : 85.86592 94.24074 85.58559 start vw surface at 0.1700000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 252894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43209 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 121767 mr = 190082 m= 33221 mr = 98069 m= 5010 mr = 25029 m= 283 mr = 3191 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 10268 time to turn everything in is 2.180000 number of dielectric boundary points 96688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 40830 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) : 1.589853 object centre at (A) : 23.41400 -18.55400 13.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6498960E-04 -1.176886 midg,1,midg; midg,igrid,midg 0.1307737 -3.3912435E-02 1,midg,midg; igrid,midg,midg 0.1183596 0.6288385 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 2.540000 now iterating at: 10:42:58 rms-change max change #iterations 11.79764 497.9490 at 10iterations 6.890263 147.0143 at 20iterations 4.001086 86.28580 at 30iterations 2.304991 53.77441 at 40iterations 1.327438 25.01762 at 50iterations 0.7612601 14.68932 at 60iterations 0.4348896 8.676000 at 70iterations 0.2481007 4.486618 at 80iterations 0.1414756 2.635120 at 90iterations 8.0604963E-02 1.409761 at 100iterations 4.5833454E-02 0.7676125 at 110iterations 2.6057443E-02 0.4420671 at 120iterations 1.4794366E-02 0.2755537 at 130iterations 8.4003070E-03 0.1600652 at 140iterations 4.7693378E-03 7.7697754E-02 at 150iterations 2.7127734E-03 4.2219162E-02 at 160iterations 1.5436311E-03 2.5742531E-02 at 170iterations 8.7925291E-04 1.5337944E-02 at 180iterations finished qdiffx linear iterations at : 10:43:15 total time elapsed so far: 20.39000 # loops : 180 mean,max change (kT/e) : 8.7925291E-04 1.5337944E-02 energy calculations done at 20.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.56000 DelPhi exited at 10:43:16 20.565u 0.494s 0:21.42 98.2% 0+0k 0+0io 0pf+0w