Sun Oct 9 15:42:46 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 15:42:46 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5503 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.4824437 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): 8.493999 62.57600 ymin,ymax (A): 53.17400 126.9650 zmin,zma (A): 29.36400 97.29700 x,y,z range (A): 54.08200 73.79100 67.93301 scale (grids/A): 0.4824437 object centre (A): 35.53500 90.06950 63.33050 number of atom coordinates read : 5503 total number of charged atoms : 5337 net assigned charge : 4.128031 assigned positive charge : 859.6235 centred at (gu) : 89.50170 90.31966 90.62533 assigned negative charge : -855.5031 centred at (gu) : 89.51570 90.29276 90.50616 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7771 nv = 96 ne = 84 npr = 110471 no. pairs analyzed = 110471 no. exposed pairs = 6705 no. arc points = 45853 no. surface atoms = 2241 nbur = 3262 mkacc time = 0.1800000 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 = 1.764000 m= 259 mr = 4066 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3500000 number of dielectric boundary points 3961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4362 ## 763 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5987369E-11 1.3902554E-10 midg,1,midg; midg,igrid,midg -7.9917791E-12 4.1527330E-11 1,midg,midg; igrid,midg,midg 3.0795873E-11 2.2418660E-12 gauss-seidel spectral radius is 0.9780822 estimated iterations to convergence 56 setup time was (sec) 0.5400000 now iterating at: 15:42:47 rms-change max change #iterations 5.5086385E-02 8.547646 at 10iterations 4.0584425E-03 0.5975437 at 20iterations 9.4461010E-04 0.1147366 at 30iterations 3.1013574E-04 4.2623997E-02 at 40iterations 1.0749062E-04 1.7054081E-02 at 50iterations finished qdiffx linear iterations at : 15:42:50 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.0749062E-04 1.7054081E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:42:50 3.618u 0.175s 0:04.21 89.7% 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 Sun Oct 9 2011 at 15:42:50 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5503 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.447331 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): 8.493999 62.57600 ymin,ymax (A): 53.17400 126.9650 zmin,zma (A): 29.36400 97.29700 x,y,z range (A): 54.08200 73.79100 67.93301 scale (grids/A): 1.447331 object centre (A): 35.53500 90.06950 63.33050 number of atom coordinates read : 5503 total number of charged atoms : 5337 net assigned charge : 4.128031 assigned positive charge : 859.6235 centred at (gu) : 88.50346 90.95714 91.87400 assigned negative charge : -855.5031 centred at (gu) : 88.54715 90.87785 91.51856 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 89669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 24587 mr = 62035 m= 1735 mr = 16296 m= 18 mr = 619 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1066 time to turn everything in is 0.4600000 number of dielectric boundary points 37059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 784 ## 18 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 39239 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) : 0.4824437 object centre at (A) : 35.53500 90.06950 63.33050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3331644E-03 8.4069120E-03 midg,1,midg; midg,igrid,midg -4.2364560E-03 5.6864013E-04 1,midg,midg; igrid,midg,midg 3.2129197E-03 1.5523832E-03 gauss-seidel spectral radius is 0.9979078 estimated iterations to convergence 174 setup time was (sec) 0.6800000 now iterating at: 15:42:51 rms-change max change #iterations 3.674479 136.1135 at 10iterations 1.434552 50.68348 at 20iterations 0.5614733 19.56316 at 30iterations 0.2206248 7.912467 at 40iterations 8.6151741E-02 2.647995 at 50iterations 3.3932701E-02 1.212569 at 60iterations 1.3444022E-02 0.4355164 at 70iterations 5.4227542E-03 0.1945496 at 80iterations 2.3038387E-03 7.6097488E-02 at 90iterations 1.0861746E-03 3.5812378E-02 at 100iterations 5.9158891E-04 1.8452644E-02 at 110iterations 3.6819902E-04 1.1545181E-02 at 120iterations finished qdiffx linear iterations at : 15:42:58 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 3.6819902E-04 1.1545181E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 15:42:59 8.030u 0.200s 0:08.53 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 15:42:59 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5503 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.170996 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): 8.493999 62.57600 ymin,ymax (A): 53.17400 126.9650 zmin,zma (A): 29.36400 97.29700 x,y,z range (A): 54.08200 73.79100 67.93301 scale (grids/A): 2.170996 object centre (A): 35.53500 90.06950 63.33050 number of atom coordinates read : 5503 total number of charged atoms : 5337 net assigned charge : 4.128031 assigned positive charge : 859.6235 centred at (gu) : 87.75471 91.43504 92.81035 assigned negative charge : -855.5031 centred at (gu) : 87.82076 91.31678 92.27765 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 209653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 90798 mr = 152846 m= 20785 mr = 70823 m= 2326 mr = 14811 m= 83 mr = 1250 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 3560 time to turn everything in is 1.060000 number of dielectric boundary points 83904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 42474 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) : 1.447331 object centre at (A) : 35.53500 90.06950 63.33050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1616018 0.1186842 midg,1,midg; midg,igrid,midg -0.1235345 -2.2437880E-02 1,midg,midg; igrid,midg,midg 6.7654088E-02 4.1626383E-02 gauss-seidel spectral radius is 0.9991089 estimated iterations to convergence 265 setup time was (sec) 1.310000 now iterating at: 15:43:00 rms-change max change #iterations 10.32288 294.5688 at 10iterations 5.786550 184.0132 at 20iterations 3.220761 74.33562 at 30iterations 1.786027 36.43900 at 40iterations 0.9859133 26.18565 at 50iterations 0.5428655 11.07913 at 60iterations 0.2989795 6.756420 at 70iterations 0.1638007 3.343733 at 80iterations 8.9633800E-02 1.690939 at 90iterations 4.8989993E-02 1.003891 at 100iterations 2.6792372E-02 0.5214778 at 110iterations 1.4613290E-02 0.2855721 at 120iterations 8.0034211E-03 0.1542130 at 130iterations 4.3678279E-03 9.0022087E-02 at 140iterations 2.3910045E-03 4.4073105E-02 at 150iterations 1.3058524E-03 2.3509860E-02 at 160iterations 7.1709295E-04 1.2958527E-02 at 170iterations 3.9517056E-04 8.1043243E-03 at 180iterations finished qdiffx linear iterations at : 15:43:12 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 3.9517056E-04 8.1043243E-03 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 15:43:13 13.163u 0.233s 0:13.83 96.8% 0+0k 0+0io 0pf+0w