Sun Oct 9 03:25:18 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 Sun Oct 9 2011 at 03:25:18 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 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: 0.5390591 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): 215.0780 275.5760 ymin,ymax (A): 73.64400 139.6850 zmin,zma (A): -70.02600 -7.953001 x,y,z range (A): 60.49800 66.04099 62.07300 scale (grids/A): 0.5390591 object centre (A): 245.3270 106.6645 -38.98950 number of atom coordinates read : 4352 total number of charged atoms : 4163 net assigned charge : 15.60002 assigned positive charge : 639.9742 centred at (gu) : 90.51020 88.14283 90.33915 assigned negative charge : -624.3787 centred at (gu) : 90.46440 88.25187 90.31378 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8040 nv = 96 ne = 84 npr = 88767 no. pairs analyzed = 88767 no. exposed pairs = 5544 no. arc points = 38539 no. surface atoms = 1890 nbur = 2462 mkacc time = 0.1900000 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 = 1.568000 m= 328 mr = 4116 m= 0 mr = 15 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3822 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9308502E-10 9.7548258E-10 midg,1,midg; midg,igrid,midg 2.3716817E-09 -3.6498544E-11 1,midg,midg; igrid,midg,midg 3.4386477E-10 1.1825073E-09 gauss-seidel spectral radius is 0.9823684 estimated iterations to convergence 62 setup time was (sec) 0.6100000 now iterating at: 03:25:19 rms-change max change #iterations 8.3320163E-02 12.48125 at 10iterations 7.4557550E-03 1.279861 at 20iterations 2.0589815E-03 0.2458057 at 30iterations 8.3039078E-04 0.1037598 at 40iterations 3.4507064E-04 4.4731140E-02 at 50iterations finished qdiffx linear iterations at : 03:25:21 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 3.4507064E-04 4.4731140E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 03:25:22 3.189u 0.146s 0:03.73 89.0% 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 Sun Oct 9 2011 at 03:25:22 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.617177 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): 215.0780 275.5760 ymin,ymax (A): 73.64400 139.6850 zmin,zma (A): -70.02600 -7.953001 x,y,z range (A): 60.49800 66.04099 62.07300 scale (grids/A): 1.617177 object centre (A): 245.3270 106.6645 -38.98950 number of atom coordinates read : 4352 total number of charged atoms : 4163 net assigned charge : 15.60002 assigned positive charge : 639.9742 centred at (gu) : 91.52901 84.42674 91.01603 assigned negative charge : -624.3787 centred at (gu) : 91.39289 84.75529 90.94112 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38539 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 28300 mr = 59823 m= 3129 mr = 19356 m= 107 mr = 1573 m= 0 mr = 12 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1316 time to turn everything in is 0.6200000 number of dielectric boundary points 39555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 31884 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) : 0.5390591 object centre at (A) : 245.3270 106.6645 -38.98950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0758698E-02 1.3151435E-02 midg,1,midg; midg,igrid,midg 4.6949141E-02 7.9952320E-03 1,midg,midg; igrid,midg,midg -2.2778210E-04 4.5594820E-03 gauss-seidel spectral radius is 0.9982984 estimated iterations to convergence 192 setup time was (sec) 0.8800000 now iterating at: 03:25:23 rms-change max change #iterations 4.007726 202.1513 at 10iterations 1.705046 56.34504 at 20iterations 0.7342865 25.76753 at 30iterations 0.3153904 9.735361 at 40iterations 0.1355982 4.579769 at 50iterations 5.8880277E-02 1.858599 at 60iterations 2.5672443E-02 0.8584270 at 70iterations 1.1477249E-02 0.4001408 at 80iterations 5.4837498E-03 0.1958981 at 90iterations 2.9370324E-03 9.1079712E-02 at 100iterations 1.7618450E-03 5.3812027E-02 at 110iterations 1.1796179E-03 3.4454346E-02 at 120iterations finished qdiffx linear iterations at : 03:25:29 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 1.1796179E-03 3.4454346E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 03:25:29 7.031u 0.152s 0:07.50 95.7% 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 03:25:29 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.425766 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): 215.0780 275.5760 ymin,ymax (A): 73.64400 139.6850 zmin,zma (A): -70.02600 -7.953001 x,y,z range (A): 60.49800 66.04099 62.07300 scale (grids/A): 2.425766 object centre (A): 245.3270 106.6645 -38.98950 number of atom coordinates read : 4352 total number of charged atoms : 4163 net assigned charge : 15.60002 assigned positive charge : 639.9742 centred at (gu) : 92.29301 81.63977 91.52355 assigned negative charge : -624.3787 centred at (gu) : 92.08910 82.13273 91.41153 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 206465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38539 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 95882 mr = 146706 m= 28558 mr = 75305 m= 5038 mr = 21406 m= 414 mr = 3376 m= 12 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 4368 time to turn everything in is 1.470000 number of dielectric boundary points 89370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 33269 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) : 1.617177 object centre at (A) : 245.3270 106.6645 -38.98950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2059499 0.1442947 midg,1,midg; midg,igrid,midg 0.6606526 0.1259190 1,midg,midg; igrid,midg,midg 3.3497147E-02 -2.8010091E-02 gauss-seidel spectral radius is 0.9992095 estimated iterations to convergence 281 setup time was (sec) 1.760000 now iterating at: 03:25:31 rms-change max change #iterations 10.53765 324.8076 at 10iterations 6.156444 153.4292 at 20iterations 3.572453 93.14697 at 30iterations 2.058233 45.08279 at 40iterations 1.180243 26.38130 at 50iterations 0.6758587 13.74231 at 60iterations 0.3852998 7.322914 at 70iterations 0.2193679 4.368370 at 80iterations 0.1248101 2.313599 at 90iterations 7.0788540E-02 1.461973 at 100iterations 4.0171642E-02 0.7803612 at 110iterations 2.2813696E-02 0.4327145 at 120iterations 1.3038654E-02 0.2262316 at 130iterations 7.4838768E-03 0.1463795 at 140iterations 4.3604122E-03 7.7013016E-02 at 150iterations 2.5973781E-03 5.0609589E-02 at 160iterations 1.6187483E-03 2.9624939E-02 at 170iterations 1.0705448E-03 2.0561218E-02 at 180iterations finished qdiffx linear iterations at : 03:25:41 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 1.0705448E-03 2.0561218E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 03:25:41 11.506u 0.157s 0:11.93 97.6% 0+0k 0+0io 0pf+0w