Tue Oct 11 03:48:08 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 Tue Oct 11 2011 at 03:48:08 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 = 2735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6639561 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): -10.99700 36.95000 ymin,ymax (A): -26.58900 23.28100 zmin,zma (A): -8.422999 45.19500 x,y,z range (A): 47.94700 49.87000 53.61800 scale (grids/A): 0.6639561 object centre (A): 12.97650 -1.653999 18.38600 number of atom coordinates read : 2735 total number of charged atoms : 2615 net assigned charge : 4.500015 assigned positive charge : 419.9686 centred at (gu) : 90.01174 89.97893 91.37695 assigned negative charge : -415.4692 centred at (gu) : 89.76541 89.84139 91.42030 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8053 nv = 96 ne = 84 npr = 55114 no. pairs analyzed = 55114 no. exposed pairs = 3443 no. arc points = 23458 no. surface atoms = 1144 nbur = 1591 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4484 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3000000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2258 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9562 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7432788E-08 3.4481482E-09 midg,1,midg; midg,igrid,midg -1.9760060E-08 4.4468997E-08 1,midg,midg; igrid,midg,midg -4.6048712E-08 6.9265688E-08 gauss-seidel spectral radius is 0.9882519 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 03:48:08 rms-change max change #iterations 0.1729959 25.92118 at 10iterations 1.8746732E-02 2.580765 at 20iterations 2.0687508E-03 0.2955856 at 30iterations 2.3639413E-04 3.7802696E-02 at 40iterations 3.1650707E-05 4.4937134E-03 at 50iterations finished qdiffx linear iterations at : 03:48:12 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 3.1650707E-05 4.4937134E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 03:48:12 4.161u 0.219s 0:04.70 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 Tue Oct 11 2011 at 03:48:12 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 = 2735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991868 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): -10.99700 36.95000 ymin,ymax (A): -26.58900 23.28100 zmin,zma (A): -8.422999 45.19500 x,y,z range (A): 47.94700 49.87000 53.61800 scale (grids/A): 1.991868 object centre (A): 12.97650 -1.653999 18.38600 number of atom coordinates read : 2735 total number of charged atoms : 2615 net assigned charge : 4.500015 assigned positive charge : 419.9686 centred at (gu) : 90.03471 89.93606 94.13024 assigned negative charge : -415.4692 centred at (gu) : 89.29591 89.52375 94.26036 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23458 grid for indexing accessible points = 1.400000 m= 32496 mr = 59872 m= 5858 mr = 24177 m= 448 mr = 3823 m= 6 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1136 time to turn everything in is 0.6800000 number of dielectric boundary points 36381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20674 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) : 0.6639561 object centre at (A) : 12.97650 -1.653999 18.38600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4380086E-02 1.1738310E-02 midg,1,midg; midg,igrid,midg -2.1657204E-02 5.4896018E-03 1,midg,midg; igrid,midg,midg -1.1126064E-02 7.1171403E-02 gauss-seidel spectral radius is 0.9987614 estimated iterations to convergence 225 setup time was (sec) 1.020000 now iterating at: 03:48:14 rms-change max change #iterations 4.845785 238.0749 at 10iterations 2.357893 78.49561 at 20iterations 1.147533 37.68716 at 30iterations 0.5574165 17.85736 at 40iterations 0.2713428 7.841208 at 50iterations 0.1316044 3.825716 at 60iterations 6.4176984E-02 2.078818 at 70iterations 3.1247854E-02 0.8744974 at 80iterations 1.5158719E-02 0.4356308 at 90iterations 7.3645492E-03 0.2074680 at 100iterations 3.5823926E-03 0.1036301 at 110iterations 1.7447441E-03 4.9007416E-02 at 120iterations finished qdiffx linear iterations at : 03:48:22 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 1.7447441E-03 4.9007416E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 03:48:23 9.786u 0.272s 0:10.50 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 Tue Oct 11 2011 at 03:48:23 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 = 2735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.987803 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): -10.99700 36.95000 ymin,ymax (A): -26.58900 23.28100 zmin,zma (A): -8.422999 45.19500 x,y,z range (A): 47.94700 49.87000 53.61800 scale (grids/A): 2.987803 object centre (A): 12.97650 -1.653999 18.38600 number of atom coordinates read : 2735 total number of charged atoms : 2615 net assigned charge : 4.500015 assigned positive charge : 419.9686 centred at (gu) : 90.05190 89.90388 96.19531 assigned negative charge : -415.4692 centred at (gu) : 88.94384 89.28556 96.39058 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 197963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23458 grid for indexing accessible points = 1.400000 m= 102970 mr = 144939 m= 39973 mr = 84533 m= 10814 mr = 32666 m= 1901 mr = 8301 m= 147 mr = 1338 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 1.760000 number of dielectric boundary points 81916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 20920 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) : 1.991868 object centre at (A) : 12.97650 -1.653999 18.38600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1961697 0.3080894 midg,1,midg; midg,igrid,midg -0.2293207 -7.2923124E-02 1,midg,midg; igrid,midg,midg -3.1373959E-02 0.5930724 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 2.100000 now iterating at: 03:48:25 rms-change max change #iterations 10.96103 363.9951 at 10iterations 6.437019 166.4550 at 20iterations 3.776870 99.43915 at 30iterations 2.215222 41.79871 at 40iterations 1.298635 23.74533 at 50iterations 0.7598386 14.72344 at 60iterations 0.4428943 7.521851 at 70iterations 0.2587977 4.491184 at 80iterations 0.1511139 2.674258 at 90iterations 8.7923817E-02 1.502434 at 100iterations 5.1378768E-02 0.8291850 at 110iterations 2.9914007E-02 0.4861946 at 120iterations 1.7449507E-02 0.2807322 at 130iterations 1.0167302E-02 0.1665559 at 140iterations 5.9425416E-03 9.9519730E-02 at 150iterations 3.4772335E-03 6.1605453E-02 at 160iterations 2.0392239E-03 3.3372879E-02 at 170iterations 1.2047547E-03 2.1762848E-02 at 180iterations finished qdiffx linear iterations at : 03:48:39 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 1.2047547E-03 2.1762848E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.97000 DelPhi exited at 03:48:40 15.971u 0.302s 0:16.60 98.0% 0+0k 0+0io 0pf+0w