Mon Oct 10 19:40:55 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 19:40:55 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 !!! WARNING: TYR 265 has a net charge of -0.2720 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: 0.5732228 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): -28.10400 29.68100 ymin,ymax (A): -17.00200 45.10300 zmin,zma (A): -31.36400 24.60900 x,y,z range (A): 57.78500 62.10500 55.97300 scale (grids/A): 0.5732228 object centre (A): 0.7884998 14.05050 -3.377501 number of atom coordinates read : 2788 total number of charged atoms : 2649 net assigned charge : -0.2719869 assigned positive charge : 411.7304 centred at (gu) : 90.93329 90.34856 90.97940 assigned negative charge : -412.0034 centred at (gu) : 90.88010 90.36839 90.93988 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6234 nv = 96 ne = 84 npr = 53970 no. pairs analyzed = 53970 no. exposed pairs = 3875 no. arc points = 28077 no. surface atoms = 1295 nbur = 1493 mkacc time = 8.9999996E-02 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= 296 mr = 3007 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2832 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7838 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5867544E-10 7.3245909E-10 midg,1,midg; midg,igrid,midg 2.3868468E-10 -4.1748502E-10 1,midg,midg; igrid,midg,midg -7.4428264E-10 9.9941500E-10 gauss-seidel spectral radius is 0.9842956 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 19:40:55 rms-change max change #iterations 9.1453820E-02 15.93022 at 10iterations 6.8009198E-03 1.198958 at 20iterations 5.2416616E-04 9.4062805E-02 at 30iterations 3.9773106E-05 7.0304871E-03 at 40iterations 2.9667078E-06 4.7588348E-04 at 50iterations finished qdiffx linear iterations at : 19:40:58 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.9667078E-06 4.7588348E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 19:40:59 3.393u 0.166s 0:04.07 87.2% 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 19:40:59 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 !!! WARNING: TYR 265 has a net charge of -0.2720 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: 1.719668 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): -28.10400 29.68100 ymin,ymax (A): -17.00200 45.10300 zmin,zma (A): -31.36400 24.60900 x,y,z range (A): 57.78500 62.10500 55.97300 scale (grids/A): 1.719668 object centre (A): 0.7884998 14.05050 -3.377501 number of atom coordinates read : 2788 total number of charged atoms : 2649 net assigned charge : -0.2719869 assigned positive charge : 411.7304 centred at (gu) : 92.79911 91.04491 92.93711 assigned negative charge : -412.0034 centred at (gu) : 92.64034 91.10474 92.81950 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28077 grid for indexing accessible points = 1.400000 m= 22020 mr = 43740 m= 3031 mr = 14997 m= 134 mr = 1630 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 32707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20521 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) : 0.5732228 object centre at (A) : 0.7884998 14.05050 -3.377501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0973832E-03 1.5083477E-02 midg,1,midg; midg,igrid,midg -2.7500346E-02 -1.1688601E-02 1,midg,midg; igrid,midg,midg -3.2463612E-03 2.4003813E-03 gauss-seidel spectral radius is 0.9983693 estimated iterations to convergence 197 setup time was (sec) 0.5500000 now iterating at: 19:41:00 rms-change max change #iterations 3.600746 162.0867 at 10iterations 1.563583 60.96789 at 20iterations 0.6811844 24.02088 at 30iterations 0.2974595 10.77627 at 40iterations 0.1295094 4.817101 at 50iterations 5.6677066E-02 2.047606 at 60iterations 2.4621287E-02 0.8614837 at 70iterations 1.0771882E-02 0.3705285 at 80iterations 4.6882709E-03 0.1619568 at 90iterations 2.0515129E-03 7.2978973E-02 at 100iterations 8.9475641E-04 3.2337189E-02 at 110iterations 3.9192953E-04 1.3282776E-02 at 120iterations finished qdiffx linear iterations at : 19:41:07 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 3.9192953E-04 1.3282776E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 19:41:07 7.725u 0.203s 0:08.42 94.0% 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 Mon Oct 10 2011 at 19:41:07 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 !!! WARNING: TYR 265 has a net charge of -0.2720 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: 2.579503 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): -28.10400 29.68100 ymin,ymax (A): -17.00200 45.10300 zmin,zma (A): -31.36400 24.60900 x,y,z range (A): 57.78500 62.10500 55.97300 scale (grids/A): 2.579503 object centre (A): 0.7884998 14.05050 -3.377501 number of atom coordinates read : 2788 total number of charged atoms : 2649 net assigned charge : -0.2719869 assigned positive charge : 411.7304 centred at (gu) : 94.19858 91.56725 94.40568 assigned negative charge : -412.0034 centred at (gu) : 93.96043 91.65715 94.22920 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 157225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28077 grid for indexing accessible points = 1.400000 m= 72679 mr = 107711 m= 24118 mr = 56165 m= 5161 mr = 18219 m= 591 mr = 3556 m= 11 mr = 298 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 73836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 21178 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) : 1.719668 object centre at (A) : 0.7884998 14.05050 -3.377501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2043131 0.2769090 midg,1,midg; midg,igrid,midg -0.3827238 -8.3237492E-02 1,midg,midg; igrid,midg,midg -6.7637734E-02 -2.8722901E-02 gauss-seidel spectral radius is 0.9991963 estimated iterations to convergence 279 setup time was (sec) 1.090000 now iterating at: 19:41:09 rms-change max change #iterations 9.126577 337.6544 at 10iterations 5.325039 139.2732 at 20iterations 3.065101 110.5265 at 30iterations 1.759644 49.43427 at 40iterations 1.001211 24.31312 at 50iterations 0.5696479 12.44920 at 60iterations 0.3216757 7.476387 at 70iterations 0.1815002 4.222862 at 80iterations 0.1024492 2.194202 at 90iterations 5.7665788E-02 1.351601 at 100iterations 3.2490440E-02 0.7089558 at 110iterations 1.8262697E-02 0.4100502 at 120iterations 1.0269335E-02 0.2179499 at 130iterations 5.7767802E-03 0.1164989 at 140iterations 3.2408098E-03 7.1910858E-02 at 150iterations 1.8172144E-03 3.6968231E-02 at 160iterations 1.0233527E-03 2.2274971E-02 at 170iterations 5.7537854E-04 1.0910988E-02 at 180iterations finished qdiffx linear iterations at : 19:41:20 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 5.7537854E-04 1.0910988E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 19:41:21 12.572u 0.212s 0:13.26 96.3% 0+0k 0+0io 0pf+0w