Mon Oct 10 17:01:04 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+sph2.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 = amb2.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 17:01:04 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: 363 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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: 0.5108264 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): -15.54700 36.58000 ymin,ymax (A): -30.57100 32.54300 zmin,zma (A): -4.089000 65.60200 x,y,z range (A): 52.12700 63.11400 69.69099 scale (grids/A): 0.5108264 object centre (A): 10.51650 0.9859991 30.75650 number of atom coordinates read : 4417 total number of charged atoms : 4211 net assigned charge : -0.1939590 assigned positive charge : 658.5459 centred at (gu) : 89.98430 90.44292 87.62987 assigned negative charge : -658.7441 centred at (gu) : 89.85290 90.54337 87.75913 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7298 nv = 96 ne = 84 npr = 89411 no. pairs analyzed = 89411 no. exposed pairs = 5769 no. arc points = 39737 no. surface atoms = 1926 nbur = 2491 mkacc time = 0.2100000 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 = 1.680000 m= 264 mr = 3724 m= 0 mr = 5 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3854 ## 579 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9815 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6250965E-10 -1.7381697E-10 midg,1,midg; midg,igrid,midg 2.0313987E-10 -2.8554573E-10 1,midg,midg; igrid,midg,midg -3.3154215E-10 2.9934533E-10 gauss-seidel spectral radius is 0.9803783 estimated iterations to convergence 59 setup time was (sec) 0.6900000 now iterating at: 17:01:05 rms-change max change #iterations 6.4953290E-02 9.411000 at 10iterations 3.7120080E-03 0.6630182 at 20iterations 2.5170794E-04 3.5453796E-02 at 30iterations 4.9258197E-05 7.2517395E-03 at 40iterations 1.8397743E-05 2.7399063E-03 at 50iterations finished qdiffx linear iterations at : 17:01:08 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.8397743E-05 2.7399063E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 17:01:10 3.660u 0.168s 0:05.21 73.3% 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 17:01:10 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: 363 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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: 1.532479 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): -15.54700 36.58000 ymin,ymax (A): -30.57100 32.54300 zmin,zma (A): -4.089000 65.60200 x,y,z range (A): 52.12700 63.11400 69.69099 scale (grids/A): 1.532479 object centre (A): 10.51650 0.9859991 30.75650 number of atom coordinates read : 4417 total number of charged atoms : 4211 net assigned charge : -0.1939590 assigned positive charge : 658.5459 centred at (gu) : 89.95125 91.32721 82.88824 assigned negative charge : -658.7441 centred at (gu) : 89.55829 91.62992 83.27735 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39737 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23929 mr = 56092 m= 2028 mr = 15765 m= 44 mr = 877 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.6400000 number of dielectric boundary points 35857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 455 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 31583 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) : 0.5108264 object centre at (A) : 10.51650 0.9859991 30.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3328508E-03 -1.3929839E-02 midg,1,midg; midg,igrid,midg 1.0665495E-02 -1.0724107E-02 1,midg,midg; igrid,midg,midg -3.8048173E-03 8.2487082E-03 gauss-seidel spectral radius is 0.9980824 estimated iterations to convergence 181 setup time was (sec) 0.9300000 now iterating at: 17:01:11 rms-change max change #iterations 3.598921 144.5284 at 10iterations 1.458479 50.26895 at 20iterations 0.5936996 19.95230 at 30iterations 0.2415463 8.606182 at 40iterations 9.8497979E-02 3.236927 at 50iterations 4.0361281E-02 1.313628 at 60iterations 1.6395353E-02 0.5337191 at 70iterations 6.6733225E-03 0.2225666 at 80iterations 2.7267693E-03 8.8064194E-02 at 90iterations 1.1149391E-03 4.0885925E-02 at 100iterations 4.5747592E-04 1.5277863E-02 at 110iterations 1.8998864E-04 6.1433315E-03 at 120iterations finished qdiffx linear iterations at : 17:01:17 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.8998864E-04 6.1433315E-03 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 17:01:18 7.667u 0.198s 0:08.56 91.7% 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 17:01:18 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: 363 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.298719 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): -15.54700 36.58000 ymin,ymax (A): -30.57100 32.54300 zmin,zma (A): -4.089000 65.60200 x,y,z range (A): 52.12700 63.11400 69.69099 scale (grids/A): 2.298719 object centre (A): 10.51650 0.9859991 30.75650 number of atom coordinates read : 4417 total number of charged atoms : 4211 net assigned charge : -0.1939590 assigned positive charge : 658.5459 centred at (gu) : 89.92645 91.99048 79.33213 assigned negative charge : -658.7441 centred at (gu) : 89.33743 92.44487 79.91590 start vw surface at 0.2500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 192499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39737 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86047 mr = 137933 m= 21680 mr = 67127 m= 3068 mr = 15423 m= 151 mr = 1894 m= 0 mr = 44 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 1.580000 number of dielectric boundary points 81024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 33588 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) : 1.532479 object centre at (A) : 10.51650 0.9859991 30.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1495245 -0.3132683 midg,1,midg; midg,igrid,midg 0.1684543 -0.2203557 1,midg,midg; igrid,midg,midg -5.7009071E-02 0.1267175 gauss-seidel spectral radius is 0.9991462 estimated iterations to convergence 270 setup time was (sec) 1.890000 now iterating at: 17:01:21 rms-change max change #iterations 9.829633 305.8353 at 10iterations 5.610200 127.2412 at 20iterations 3.173640 66.99503 at 30iterations 1.789051 43.90359 at 40iterations 1.002837 25.43445 at 50iterations 0.5604272 11.89212 at 60iterations 0.3124034 6.319586 at 70iterations 0.1736763 3.686900 at 80iterations 9.6554786E-02 1.937111 at 90iterations 5.3619705E-02 1.054260 at 100iterations 2.9673150E-02 0.5595169 at 110iterations 1.6404789E-02 0.3812294 at 120iterations 9.0986528E-03 0.1859665 at 130iterations 5.0302520E-03 9.9264145E-02 at 140iterations 2.7737368E-03 5.7403564E-02 at 150iterations 1.5389061E-03 3.6231995E-02 at 160iterations 8.5170055E-04 1.7246246E-02 at 170iterations 4.7243934E-04 1.0326385E-02 at 180iterations finished qdiffx linear iterations at : 17:01:31 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 4.7243934E-04 1.0326385E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 17:01:32 12.877u 0.212s 0:13.61 96.1% 0+0k 0+0io 0pf+0w