Sat Oct 15 14:13:11 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 Sat Oct 15 2011 at 14:13:11 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4581 !!! WARNING: HEM 810 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5227453 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): -24.71100 40.01300 ymin,ymax (A): -18.17800 46.73200 zmin,zma (A): 7.104001 75.20600 x,y,z range (A): 64.72400 64.91000 68.10200 scale (grids/A): 0.5227453 object centre (A): 7.651000 14.27700 41.15500 number of atom coordinates read : 4581 total number of charged atoms : 4341 net assigned charge : 7.800027 assigned positive charge : 693.0057 centred at (gu) : 91.39558 88.94238 87.72676 assigned negative charge : -685.2096 centred at (gu) : 91.50458 89.04839 87.58844 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8145 nv = 96 ne = 84 npr = 91079 no. pairs analyzed = 91079 no. exposed pairs = 6090 no. arc points = 41631 no. surface atoms = 2037 nbur = 2544 mkacc time = 0.1600000 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 = 1.624000 m= 304 mr = 4159 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4062 ## 578 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9021910E-10 4.2414794E-10 midg,1,midg; midg,igrid,midg 8.2953866E-10 -1.7727508E-10 1,midg,midg; igrid,midg,midg 4.4896717E-10 -3.6362291E-10 gauss-seidel spectral radius is 0.9812734 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 14:13:12 rms-change max change #iterations 7.4011490E-02 10.15338 at 10iterations 4.8459270E-03 0.6354218 at 20iterations 8.7700423E-04 0.1218462 at 30iterations 3.4617167E-04 5.2232742E-02 at 40iterations 1.4482686E-04 2.2286415E-02 at 50iterations finished qdiffx linear iterations at : 14:13:15 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 1.4482686E-04 2.2286415E-02 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 14:13:16 3.751u 0.207s 0:04.34 91.0% 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 Sat Oct 15 2011 at 14:13:16 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4581 !!! WARNING: HEM 810 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.568236 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): -24.71100 40.01300 ymin,ymax (A): -18.17800 46.73200 zmin,zma (A): 7.104001 75.20600 x,y,z range (A): 64.72400 64.91000 68.10200 scale (grids/A): 1.568236 object centre (A): 7.651000 14.27700 41.15500 number of atom coordinates read : 4581 total number of charged atoms : 4341 net assigned charge : 7.800027 assigned positive charge : 693.0057 centred at (gu) : 94.18512 86.82561 83.17906 assigned negative charge : -685.2096 centred at (gu) : 94.51331 87.14468 82.76493 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26895 mr = 61781 m= 2432 mr = 17908 m= 44 mr = 1009 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 0.4600000 number of dielectric boundary points 39805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 32925 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) : 0.5227453 object centre at (A) : 7.651000 14.27700 41.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9835299E-03 2.2600515E-02 midg,1,midg; midg,igrid,midg 4.9688988E-03 -8.8658286E-03 1,midg,midg; igrid,midg,midg 1.2818987E-02 2.7028441E-03 gauss-seidel spectral radius is 0.9981947 estimated iterations to convergence 187 setup time was (sec) 0.7000000 now iterating at: 14:13:17 rms-change max change #iterations 3.925090 168.9428 at 10iterations 1.642938 66.02684 at 20iterations 0.6853489 23.13546 at 30iterations 0.2878609 10.30324 at 40iterations 0.1198772 3.726984 at 50iterations 5.0461486E-02 1.554317 at 60iterations 2.1219086E-02 0.6416385 at 70iterations 9.0326034E-03 0.3095264 at 80iterations 3.9294418E-03 0.1290092 at 90iterations 1.8441862E-03 6.5059662E-02 at 100iterations 9.7503513E-04 3.5921097E-02 at 110iterations 6.0416490E-04 2.0477295E-02 at 120iterations finished qdiffx linear iterations at : 14:13:25 total time elapsed so far: 8.430000 # loops : 120 mean,max change (kT/e) : 6.0416490E-04 2.0477295E-02 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 14:13:25 8.563u 0.266s 0:09.60 91.8% 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 Sat Oct 15 2011 at 14:13:25 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4581 !!! WARNING: HEM 810 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.352354 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): -24.71100 40.01300 ymin,ymax (A): -18.17800 46.73200 zmin,zma (A): 7.104001 75.20600 x,y,z range (A): 64.72400 64.91000 68.10200 scale (grids/A): 2.352354 object centre (A): 7.651000 14.27700 41.15500 number of atom coordinates read : 4581 total number of charged atoms : 4341 net assigned charge : 7.800027 assigned positive charge : 693.0057 centred at (gu) : 96.27745 85.23814 79.76833 assigned negative charge : -685.2096 centred at (gu) : 96.76975 85.71698 79.14725 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 212013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 95633 mr = 152100 m= 24577 mr = 74295 m= 3534 mr = 17621 m= 231 mr = 2174 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 983 time to turn everything in is 1.150000 number of dielectric boundary points 89712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 34671 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) : 1.568236 object centre at (A) : 7.651000 14.27700 41.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4848479 0.5162480 midg,1,midg; midg,igrid,midg 1.1750615E-02 -0.1888621 1,midg,midg; igrid,midg,midg 0.2051927 7.2959960E-02 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 1.400000 now iterating at: 14:13:27 rms-change max change #iterations 10.43929 261.1617 at 10iterations 6.012346 165.8605 at 20iterations 3.444184 70.51150 at 30iterations 1.959615 43.20682 at 40iterations 1.109985 27.46730 at 50iterations 0.6277468 14.73446 at 60iterations 0.3538370 7.342162 at 70iterations 0.1994968 4.085693 at 80iterations 0.1121699 2.234857 at 90iterations 6.3011549E-02 1.251822 at 100iterations 3.5450853E-02 0.7571640 at 110iterations 1.9895725E-02 0.3812256 at 120iterations 1.1140257E-02 0.1975288 at 130iterations 6.2439512E-03 0.1216125 at 140iterations 3.5139190E-03 6.7517281E-02 at 150iterations 1.9738358E-03 4.0641785E-02 at 160iterations 1.1159626E-03 2.1432877E-02 at 170iterations 6.3858257E-04 1.2283325E-02 at 180iterations finished qdiffx linear iterations at : 14:13:43 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 6.3858257E-04 1.2283325E-02 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.45000 DelPhi exited at 14:13:44 15.453u 0.310s 0:18.59 84.7% 0+0k 0+0io 0pf+0w