Mon Oct 10 17:02:46 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+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 Mon Oct 10 2011 at 17:02:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 0.5826323 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): -11.33200 49.77000 ymin,ymax (A): -7.433000 41.45000 zmin,zma (A): 0.4030000 56.27800 x,y,z range (A): 61.10200 48.88300 55.87500 scale (grids/A): 0.5826323 object centre (A): 19.21900 17.00850 28.34050 number of atom coordinates read : 3016 total number of charged atoms : 2873 net assigned charge : -4.499968 assigned positive charge : 452.8698 centred at (gu) : 89.97746 89.49023 88.53023 assigned negative charge : -457.3711 centred at (gu) : 89.91911 89.38074 88.47200 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 6725 nv = 96 ne = 84 npr = 60213 no. pairs analyzed = 60213 no. exposed pairs = 4045 no. arc points = 28699 no. surface atoms = 1367 nbur = 1649 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 = 1.484000 m= 298 mr = 3342 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2910 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 8602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4975338E-09 2.6444341E-10 midg,1,midg; midg,igrid,midg -4.2455417E-09 1.4395483E-09 1,midg,midg; igrid,midg,midg -2.4935163E-09 3.9249504E-10 gauss-seidel spectral radius is 0.9848028 estimated iterations to convergence 67 setup time was (sec) 0.7600000 now iterating at: 17:02:47 rms-change max change #iterations 9.8194949E-02 17.18981 at 10iterations 7.7672480E-03 1.159880 at 20iterations 6.2320859E-04 9.8869324E-02 at 30iterations 5.0314029E-05 7.6751709E-03 at 40iterations 5.2932587E-06 1.1749268E-03 at 50iterations finished qdiffx linear iterations at : 17:02:51 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 5.2932587E-06 1.1749268E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 17:02:52 4.326u 0.198s 0:05.53 81.5% 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 17:02:52 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 = 3016 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: 1.747897 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): -11.33200 49.77000 ymin,ymax (A): -7.433000 41.45000 zmin,zma (A): 0.4030000 56.27800 x,y,z range (A): 61.10200 48.88300 55.87500 scale (grids/A): 1.747897 object centre (A): 19.21900 17.00850 28.34050 number of atom coordinates read : 3016 total number of charged atoms : 2873 net assigned charge : -4.499968 assigned positive charge : 452.8698 centred at (gu) : 89.93189 88.46974 85.58990 assigned negative charge : -457.3711 centred at (gu) : 89.75701 88.14170 85.41570 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 73534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28699 grid for indexing accessible points = 1.400000 m= 22937 mr = 48426 m= 2701 mr = 15683 m= 96 mr = 1326 m= 0 mr = 11 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 774 time to turn everything in is 0.6800000 number of dielectric boundary points 33822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22348 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) : 0.5826323 object centre at (A) : 19.21900 17.00850 28.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7323755E-03 -1.0694959E-03 midg,1,midg; midg,igrid,midg -1.8513352E-02 4.5089712E-03 1,midg,midg; igrid,midg,midg -3.5213333E-02 1.0386758E-02 gauss-seidel spectral radius is 0.9984327 estimated iterations to convergence 200 setup time was (sec) 1.050000 now iterating at: 17:02:53 rms-change max change #iterations 3.906430 203.7620 at 10iterations 1.717506 66.68228 at 20iterations 0.7637155 29.14294 at 30iterations 0.3380469 11.32117 at 40iterations 0.1491040 4.972771 at 50iterations 6.6177480E-02 2.353424 at 60iterations 2.9264716E-02 0.9237747 at 70iterations 1.2972298E-02 0.4435492 at 80iterations 5.7481197E-03 0.1994152 at 90iterations 2.5540884E-03 9.0270996E-02 at 100iterations 1.1345822E-03 3.9964676E-02 at 110iterations 5.0408480E-04 1.6718149E-02 at 120iterations finished qdiffx linear iterations at : 17:03:02 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 5.0408480E-04 1.6718149E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 17:03:03 9.612u 0.254s 0:10.81 91.2% 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 17:03:03 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 = 3016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.621845 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): -11.33200 49.77000 ymin,ymax (A): -7.433000 41.45000 zmin,zma (A): 0.4030000 56.27800 x,y,z range (A): 61.10200 48.88300 55.87500 scale (grids/A): 2.621845 object centre (A): 19.21900 17.00850 28.34050 number of atom coordinates read : 3016 total number of charged atoms : 2873 net assigned charge : -4.499968 assigned positive charge : 452.8698 centred at (gu) : 89.89745 87.70436 83.38474 assigned negative charge : -457.3711 centred at (gu) : 89.63554 87.21240 83.12347 start vw surface at 0.2400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 170456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28699 grid for indexing accessible points = 1.400000 m= 77854 mr = 118844 m= 23656 mr = 60590 m= 4267 mr = 17874 m= 375 mr = 2808 m= 4 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 2430 time to turn everything in is 1.670000 number of dielectric boundary points 76343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 22980 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) : 1.747897 object centre at (A) : 19.21900 17.00850 28.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2257380 -9.7508326E-02 midg,1,midg; midg,igrid,midg -0.1948407 7.8440674E-02 1,midg,midg; igrid,midg,midg -0.4372253 0.2292315 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 2.060000 now iterating at: 17:03:05 rms-change max change #iterations 9.850559 329.2503 at 10iterations 5.751201 172.4392 at 20iterations 3.322975 73.48061 at 30iterations 1.909335 44.19431 at 40iterations 1.095641 23.35071 at 50iterations 0.6271852 12.45809 at 60iterations 0.3573948 9.536389 at 70iterations 0.2034538 4.771637 at 80iterations 0.1158937 2.438874 at 90iterations 6.5812610E-02 1.502487 at 100iterations 3.7498288E-02 0.7588124 at 110iterations 2.1259518E-02 0.4079494 at 120iterations 1.2050777E-02 0.2426808 at 130iterations 6.8416181E-03 0.1496658 at 140iterations 3.8701782E-03 7.8399658E-02 at 150iterations 2.1968749E-03 4.3479919E-02 at 160iterations 1.2474461E-03 2.3933411E-02 at 170iterations 7.0699467E-04 1.3068676E-02 at 180iterations finished qdiffx linear iterations at : 17:03:18 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 7.0699467E-04 1.3068676E-02 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.41000 DelPhi exited at 17:03:21 15.407u 0.233s 0:17.77 87.9% 0+0k 0+0io 0pf+0w