Mon Oct 10 14:38:00 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 14:38:00 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3709 !!! WARNING: GLN 328 has a net charge of -0.2720 !!! WARNING: ADP 1298 has a net charge of -2.0000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: MG1 1302 has a net charge of 1.4000 !!! WARNING: MG1 1303 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: 0.3440578 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): -12.69500 57.02800 ymin,ymax (A): 2.270000 65.40700 zmin,zma (A): -4.964000 98.50700 x,y,z range (A): 69.72300 63.13700 103.4710 scale (grids/A): 0.3440578 object centre (A): 22.16650 33.83850 46.77150 number of atom coordinates read : 3709 total number of charged atoms : 3475 net assigned charge : -2.571983 assigned positive charge : 575.1190 centred at (gu) : 87.62553 89.72401 84.50445 assigned negative charge : -577.6927 centred at (gu) : 87.61581 89.75999 84.45187 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 2536 nv = 96 ne = 84 npr = 68918 no. pairs analyzed = 68918 no. exposed pairs = 5623 no. arc points = 39931 no. surface atoms = 1866 nbur = 1843 mkacc time = 0.2000000 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 = 2.436000 m= 48 mr = 895 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 1689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2399 ## 780 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 3613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7425121E-14 2.7749517E-16 midg,1,midg; midg,igrid,midg 1.5274290E-15 -2.0300815E-15 1,midg,midg; igrid,midg,midg -2.2860180E-15 1.7728391E-17 gauss-seidel spectral radius is 0.9573396 estimated iterations to convergence 41 setup time was (sec) 0.7500000 now iterating at: 14:38:01 rms-change max change #iterations 6.1419541E-03 1.763172 at 10iterations 2.0732246E-04 7.4165344E-02 at 20iterations 2.1142310E-05 7.1249008E-03 at 30iterations 2.4253227E-06 7.9822540E-04 at 40iterations 2.7934706E-07 9.3460083E-05 at 50iterations finished qdiffx linear iterations at : 14:38:04 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 2.7934706E-07 9.3460083E-05 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 14:38:05 4.537u 0.208s 0:05.10 92.7% 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 Mon Oct 10 2011 at 14:38:05 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3709 !!! WARNING: GLN 328 has a net charge of -0.2720 !!! WARNING: ADP 1298 has a net charge of -2.0000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: MG1 1302 has a net charge of 1.4000 !!! WARNING: MG1 1303 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.032173 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): -12.69500 57.02800 ymin,ymax (A): 2.270000 65.40700 zmin,zma (A): -4.964000 98.50700 x,y,z range (A): 69.72300 63.13700 103.4710 scale (grids/A): 1.032173 object centre (A): 22.16650 33.83850 46.77150 number of atom coordinates read : 3709 total number of charged atoms : 3475 net assigned charge : -2.571983 assigned positive charge : 575.1190 centred at (gu) : 82.87572 89.17147 73.51207 assigned negative charge : -577.6927 centred at (gu) : 82.84721 89.27964 73.35490 start vw surface at 0.2400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 30570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.358720 m= 4619 mr = 17027 m= 128 mr = 1873 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.4500000 number of dielectric boundary points 16417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1244 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20956 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) : 0.3440578 object centre at (A) : 22.16650 33.83850 46.77150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2884571E-04 2.5060661E-05 midg,1,midg; midg,igrid,midg -1.1501761E-04 -2.6115190E-04 1,midg,midg; igrid,midg,midg -1.4157000E-04 2.8947563E-05 gauss-seidel spectral radius is 0.9952911 estimated iterations to convergence 117 setup time was (sec) 0.8000000 now iterating at: 14:38:06 rms-change max change #iterations 1.129004 95.31779 at 10iterations 0.2737251 19.12715 at 20iterations 6.6915572E-02 4.476151 at 30iterations 1.6464772E-02 1.022496 at 40iterations 4.0960093E-03 0.2336617 at 50iterations 1.1212004E-03 8.1489563E-02 at 60iterations 3.7473452E-04 2.7903557E-02 at 70iterations 1.6584109E-04 1.2272835E-02 at 80iterations 8.4927560E-05 5.9299469E-03 at 90iterations 4.5299352E-05 3.2157898E-03 at 100iterations 2.4406980E-05 1.7471313E-03 at 110iterations 1.3175099E-05 9.5081329E-04 at 120iterations finished qdiffx linear iterations at : 14:38:14 total time elapsed so far: 8.890000 # loops : 120 mean,max change (kT/e) : 1.3175099E-05 9.5081329E-04 energy calculations done at 8.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.130000 DelPhi exited at 14:38:15 9.136u 0.223s 0:10.06 92.9% 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 14:38:15 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3709 !!! WARNING: GLN 328 has a net charge of -0.2720 !!! WARNING: ADP 1298 has a net charge of -2.0000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: MG1 1302 has a net charge of 1.4000 !!! WARNING: MG1 1303 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: 1.548260 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): -12.69500 57.02800 ymin,ymax (A): 2.270000 65.40700 zmin,zma (A): -4.964000 98.50700 x,y,z range (A): 69.72300 63.13700 103.4710 scale (grids/A): 1.548260 object centre (A): 22.16650 33.83850 46.77150 number of atom coordinates read : 3709 total number of charged atoms : 3475 net assigned charge : -2.571983 assigned positive charge : 575.1190 centred at (gu) : 79.31329 88.75702 65.26785 assigned negative charge : -577.6927 centred at (gu) : 79.27081 88.91932 65.03230 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 72539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.329600 m= 20260 mr = 44549 m= 1834 mr = 12181 m= 35 mr = 764 m= 0 mr = 2 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.8500000 number of dielectric boundary points 37172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 576 ## 13 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 26196 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) : 1.032173 object centre at (A) : 22.16650 33.83850 46.77150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7905606E-02 1.0185032E-03 midg,1,midg; midg,igrid,midg -6.5482198E-03 -1.6268540E-02 1,midg,midg; igrid,midg,midg -6.8526198E-03 1.6718530E-03 gauss-seidel spectral radius is 0.9979873 estimated iterations to convergence 177 setup time was (sec) 1.220000 now iterating at: 14:38:17 rms-change max change #iterations 4.140096 201.3824 at 10iterations 1.709022 73.82693 at 20iterations 0.6985870 35.43027 at 30iterations 0.2853527 10.95986 at 40iterations 0.1151728 4.398860 at 50iterations 4.6351727E-02 1.913685 at 60iterations 1.8705038E-02 0.7363892 at 70iterations 7.5314371E-03 0.2645111 at 80iterations 3.0533436E-03 0.1200085 at 90iterations 1.2544540E-03 5.1740885E-02 at 100iterations 5.4218620E-04 2.1252632E-02 at 110iterations 2.5648403E-04 1.1556625E-02 at 120iterations 1.3893447E-04 6.2885284E-03 at 130iterations 8.4531632E-05 3.9196014E-03 at 140iterations 5.5130855E-05 2.5415421E-03 at 150iterations 3.6997993E-05 1.7080307E-03 at 160iterations 2.5049596E-05 1.1606216E-03 at 170iterations 1.7042381E-05 7.8773499E-04 at 180iterations finished qdiffx linear iterations at : 14:38:29 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 1.7042381E-05 7.8773499E-04 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 14:38:30 13.943u 0.235s 0:14.60 97.0% 0+0k 0+0io 0pf+0w