Sun Oct 9 12:00:22 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 12:00:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6897888 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): -5.199000 43.61900 ymin,ymax (A): -14.28800 37.32200 zmin,zma (A): 1.310000 45.38600 x,y,z range (A): 48.81800 51.61000 44.07600 scale (grids/A): 0.6897888 object centre (A): 19.21000 11.51700 23.34800 number of atom coordinates read : 2374 total number of charged atoms : 2233 net assigned charge : 3.500020 assigned positive charge : 361.0341 centred at (gu) : 89.19696 90.84604 90.70899 assigned negative charge : -357.5346 centred at (gu) : 89.22305 91.01460 90.75012 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7600 nv = 96 ne = 84 npr = 48041 no. pairs analyzed = 48041 no. exposed pairs = 2911 no. arc points = 20457 no. surface atoms = 982 nbur = 1392 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 4249 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.1800000 number of dielectric boundary points 3755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1967 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8645 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0782839E-08 4.8169233E-09 midg,1,midg; midg,igrid,midg 6.9644770E-08 -5.3597653E-08 1,midg,midg; igrid,midg,midg 3.4867423E-08 8.6912593E-09 gauss-seidel spectral radius is 0.9890797 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 12:00:23 rms-change max change #iterations 0.1875642 27.70582 at 10iterations 2.2738235E-02 3.170042 at 20iterations 3.1611542E-03 0.5008316 at 30iterations 6.6196366E-04 0.1088791 at 40iterations 2.0037663E-04 3.2718658E-02 at 50iterations finished qdiffx linear iterations at : 12:00:26 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.0037663E-04 3.2718658E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 12:00:26 3.343u 0.172s 0:03.82 91.8% 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 12:00:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.069366 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): -5.199000 43.61900 ymin,ymax (A): -14.28800 37.32200 zmin,zma (A): 1.310000 45.38600 x,y,z range (A): 48.81800 51.61000 44.07600 scale (grids/A): 2.069366 object centre (A): 19.21000 11.51700 23.34800 number of atom coordinates read : 2374 total number of charged atoms : 2233 net assigned charge : 3.500020 assigned positive charge : 361.0341 centred at (gu) : 87.59044 92.53758 92.12650 assigned negative charge : -357.5346 centred at (gu) : 87.66877 93.04373 92.25016 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20457 grid for indexing accessible points = 1.400000 m= 30459 mr = 56034 m= 5157 mr = 22792 m= 423 mr = 3311 m= 3 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3806 time to turn everything in is 0.4000000 number of dielectric boundary points 34236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17742 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) : 0.6897888 object centre at (A) : 19.21000 11.51700 23.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0489392E-02 1.5210059E-02 midg,1,midg; midg,igrid,midg 1.7235214E-02 -4.6377786E-02 1,midg,midg; igrid,midg,midg 4.7990769E-02 -9.9489195E-03 gauss-seidel spectral radius is 0.9988117 estimated iterations to convergence 230 setup time was (sec) 0.6100000 now iterating at: 12:00:27 rms-change max change #iterations 4.765213 196.9901 at 10iterations 2.344977 74.57602 at 20iterations 1.154546 39.79189 at 30iterations 0.5674875 15.91101 at 40iterations 0.2797587 8.538128 at 50iterations 0.1380180 4.037521 at 60iterations 6.8185754E-02 1.935528 at 70iterations 3.3655435E-02 1.030195 at 80iterations 1.6772425E-02 0.5064230 at 90iterations 8.3814925E-03 0.2392130 at 100iterations 4.2547612E-03 0.1367111 at 110iterations 2.2101738E-03 6.8367004E-02 at 120iterations finished qdiffx linear iterations at : 12:00:34 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.2101738E-03 6.8367004E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 12:00:34 7.956u 0.208s 0:08.43 96.6% 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 12:00:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.104050 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): -5.199000 43.61900 ymin,ymax (A): -14.28800 37.32200 zmin,zma (A): 1.310000 45.38600 x,y,z range (A): 48.81800 51.61000 44.07600 scale (grids/A): 3.104050 object centre (A): 19.21000 11.51700 23.34800 number of atom coordinates read : 2374 total number of charged atoms : 2233 net assigned charge : 3.500020 assigned positive charge : 361.0341 centred at (gu) : 86.38556 93.80618 93.18976 assigned negative charge : -357.5346 centred at (gu) : 86.50320 94.56545 93.37526 start vw surface at 0.1100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 185654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20457 grid for indexing accessible points = 1.400000 m= 96961 mr = 135324 m= 36849 mr = 79928 m= 9462 mr = 29989 m= 1736 mr = 7200 m= 180 mr = 1273 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 12469 time to turn everything in is 1.240000 number of dielectric boundary points 77018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 17864 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) : 2.069366 object centre at (A) : 19.21000 11.51700 23.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4487976 3.6289860E-02 midg,1,midg; midg,igrid,midg 0.3488410 -0.5288255 1,midg,midg; igrid,midg,midg 0.4877510 -0.2923119 gauss-seidel spectral radius is 0.9992936 estimated iterations to convergence 297 setup time was (sec) 1.470000 now iterating at: 12:00:36 rms-change max change #iterations 10.71993 510.2961 at 10iterations 6.328650 132.3412 at 20iterations 3.728097 72.17630 at 30iterations 2.194391 43.25121 at 40iterations 1.288164 22.86592 at 50iterations 0.7557790 13.62038 at 60iterations 0.4429264 8.302863 at 70iterations 0.2593724 4.972109 at 80iterations 0.1516893 2.647812 at 90iterations 8.8838890E-02 1.497669 at 100iterations 5.2208971E-02 0.9609833 at 110iterations 3.0577306E-02 0.5719700 at 120iterations 1.8235121E-02 0.3178101 at 130iterations 1.0968504E-02 0.2157860 at 140iterations 6.8055913E-03 0.1267433 at 150iterations 4.4012009E-03 8.5613251E-02 at 160iterations 3.0158525E-03 6.0646057E-02 at 170iterations 2.1946998E-03 5.1116943E-02 at 180iterations finished qdiffx linear iterations at : 12:00:48 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 2.1946998E-03 5.1116943E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 12:00:48 13.079u 0.199s 0:13.55 97.8% 0+0k 0+0io 0pf+0w