Mon Oct 10 17:01:40 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 17:01:40 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4394 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5146293 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): -16.52800 36.83400 ymin,ymax (A): -33.06800 31.43700 zmin,zma (A): -3.815000 65.36100 x,y,z range (A): 53.36200 64.50500 69.17600 scale (grids/A): 0.5146293 object centre (A): 10.15300 -0.8155003 30.77300 number of atom coordinates read : 4394 total number of charged atoms : 4146 net assigned charge : 3.606024 assigned positive charge : 655.2953 centred at (gu) : 90.30489 91.10461 87.57118 assigned negative charge : -651.6932 centred at (gu) : 90.16389 91.14046 87.59151 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7321 nv = 96 ne = 84 npr = 89770 no. pairs analyzed = 89770 no. exposed pairs = 5674 no. arc points = 39253 no. surface atoms = 1890 nbur = 2504 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 = 1.652000 m= 274 mr = 3718 m= 0 mr = 10 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3724 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1922660E-10 2.2473295E-12 midg,1,midg; midg,igrid,midg 1.1899981E-10 -5.6134521E-11 1,midg,midg; igrid,midg,midg -3.1379696E-10 4.8151561E-10 gauss-seidel spectral radius is 0.9806609 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 17:01:41 rms-change max change #iterations 6.9455802E-02 12.69460 at 10iterations 4.1873381E-03 0.6634445 at 20iterations 5.1911850E-04 7.0313454E-02 at 30iterations 1.7269078E-04 2.2079468E-02 at 40iterations 6.3627107E-05 8.6815357E-03 at 50iterations finished qdiffx linear iterations at : 17:01:44 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 6.3627107E-05 8.6815357E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 17:01:45 3.543u 0.193s 0:04.41 84.5% 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 17:01:45 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4394 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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: 1.543888 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): -16.52800 36.83400 ymin,ymax (A): -33.06800 31.43700 zmin,zma (A): -3.815000 65.36100 x,y,z range (A): 53.36200 64.50500 69.17600 scale (grids/A): 1.543888 object centre (A): 10.15300 -0.8155003 30.77300 number of atom coordinates read : 4394 total number of charged atoms : 4146 net assigned charge : 3.606024 assigned positive charge : 655.2953 centred at (gu) : 90.91325 93.31281 82.71228 assigned negative charge : -651.6932 centred at (gu) : 90.49164 93.42113 82.77413 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23733 mr = 56495 m= 1978 mr = 15363 m= 39 mr = 768 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 36094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 509 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 31240 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) : 0.5146293 object centre at (A) : 10.15300 -0.8155003 30.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1362906E-03 8.6604105E-03 midg,1,midg; midg,igrid,midg -1.1183455E-03 -1.2317134E-02 1,midg,midg; igrid,midg,midg -4.6963659E-03 9.7338995E-03 gauss-seidel spectral radius is 0.9981062 estimated iterations to convergence 183 setup time was (sec) 0.6300000 now iterating at: 17:01:45 rms-change max change #iterations 3.671520 149.8774 at 10iterations 1.494990 52.70700 at 20iterations 0.6121216 21.60525 at 30iterations 0.2506221 8.842659 at 40iterations 0.1026608 3.844330 at 50iterations 4.2160481E-02 1.331795 at 60iterations 1.7228335E-02 0.5576055 at 70iterations 7.0904205E-03 0.2364273 at 80iterations 2.9245587E-03 0.1015224 at 90iterations 1.2215696E-03 4.2406082E-02 at 100iterations 5.2420620E-04 1.7309189E-02 at 110iterations 2.4079470E-04 7.6463223E-03 at 120iterations finished qdiffx linear iterations at : 17:01:53 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.4079470E-04 7.6463223E-03 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 17:01:53 7.876u 0.231s 0:08.83 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 17:01:54 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4394 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.315832 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): -16.52800 36.83400 ymin,ymax (A): -33.06800 31.43700 zmin,zma (A): -3.815000 65.36100 x,y,z range (A): 53.36200 64.50500 69.17600 scale (grids/A): 2.315832 object centre (A): 10.15300 -0.8155003 30.77300 number of atom coordinates read : 4394 total number of charged atoms : 4146 net assigned charge : 3.606024 assigned positive charge : 655.2953 centred at (gu) : 91.36952 94.96897 79.06812 assigned negative charge : -651.6932 centred at (gu) : 90.73738 95.13166 79.16117 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 193495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85037 mr = 139083 m= 20639 mr = 65696 m= 2833 mr = 14365 m= 164 mr = 1595 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 81362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 33052 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) : 1.543888 object centre at (A) : 10.15300 -0.8155003 30.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1565585 0.2491152 midg,1,midg; midg,igrid,midg -6.5081537E-02 -0.3114574 1,midg,midg; igrid,midg,midg -6.5245613E-02 0.1313435 gauss-seidel spectral radius is 0.9991525 estimated iterations to convergence 271 setup time was (sec) 1.230000 now iterating at: 17:01:55 rms-change max change #iterations 9.972645 254.7863 at 10iterations 5.693965 131.0122 at 20iterations 3.224936 72.44707 at 30iterations 1.818839 44.65068 at 40iterations 1.024234 21.53978 at 50iterations 0.5730317 12.56686 at 60iterations 0.3199459 7.155490 at 70iterations 0.1779995 3.674777 at 80iterations 9.9218093E-02 2.014824 at 90iterations 5.5053871E-02 1.147956 at 100iterations 3.0596266E-02 0.5962677 at 110iterations 1.6985111E-02 0.3545456 at 120iterations 9.4182389E-03 0.1834002 at 130iterations 5.2166772E-03 0.1060219 at 140iterations 2.8893596E-03 5.9253693E-02 at 150iterations 1.6068944E-03 3.6895752E-02 at 160iterations 8.9046109E-04 1.7135620E-02 at 170iterations 4.9610971E-04 9.3936920E-03 at 180iterations finished qdiffx linear iterations at : 17:02:07 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 4.9610971E-04 9.3936920E-03 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 17:02:07 12.990u 0.217s 0:13.56 97.3% 0+0k 0+0io 0pf+0w