Wed Feb 15 08:55:37 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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: 0.5392305 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 0.5392305 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.22553 90.96852 89.71351 assigned negative charge : -727.2772 centred at (gu) : 90.21529 90.93708 89.74884 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8785 nv = 96 ne = 84 npr = 99961 no. pairs analyzed = 99961 no. exposed pairs = 5797 no. arc points = 38874 no. surface atoms = 1953 nbur = 2850 mkacc time = 0.1700000 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 = 1.596000 m= 323 mr = 4801 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3884 ## 474 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 11748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6294128E-10 -3.2604938E-10 midg,1,midg; midg,igrid,midg -2.4887092E-10 2.7209737E-10 1,midg,midg; igrid,midg,midg -1.3058504E-10 3.6494620E-11 gauss-seidel spectral radius is 0.9823999 estimated iterations to convergence 62 setup time was (sec) 0.5200000 now iterating at: 08:55:39 rms-change max change #iterations 8.7239429E-02 11.52637 at 10iterations 5.9515201E-03 1.005539 at 20iterations 7.0827641E-04 0.1178818 at 30iterations 2.4314549E-04 3.3960342E-02 at 40iterations 1.0818185E-04 1.5469551E-02 at 50iterations finished qdiffx linear iterations at : 08:55:42 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.0818185E-04 1.5469551E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:55:43 3.553u 0.181s 0:04.53 82.3% 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 Wed Feb 15 2012 at 08:55:43 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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: 1.617692 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 1.617692 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.67482 92.90411 89.13883 assigned negative charge : -727.2772 centred at (gu) : 90.64532 92.81075 89.24642 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 99165 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38874 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31254 mr = 70394 m= 3256 mr = 21736 m= 87 mr = 1591 m= 0 mr = 9 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 860 time to turn everything in is 0.4900000 number of dielectric boundary points 40032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 35502 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) : 0.5392305 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7411115E-03 6.2881587E-03 midg,1,midg; midg,igrid,midg -6.3701747E-03 -1.0357205E-02 1,midg,midg; igrid,midg,midg -3.3657283E-02 1.3535218E-03 gauss-seidel spectral radius is 0.9983255 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 08:55:44 rms-change max change #iterations 4.299021 162.3490 at 10iterations 1.859258 63.19970 at 20iterations 0.8023263 23.30313 at 30iterations 0.3468798 11.77544 at 40iterations 0.1499804 4.471581 at 50iterations 6.4982608E-02 2.025567 at 60iterations 2.8185545E-02 0.8722801 at 70iterations 1.2279967E-02 0.3793564 at 80iterations 5.4055951E-03 0.1618347 at 90iterations 2.4398905E-03 7.4420929E-02 at 100iterations 1.1703387E-03 3.9396524E-02 at 110iterations 6.4501335E-04 2.2229910E-02 at 120iterations finished qdiffx linear iterations at : 08:55:51 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 6.4501335E-04 2.2229910E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 08:55:52 8.020u 0.219s 0:09.07 90.7% 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 Wed Feb 15 2012 at 08:55:52 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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: 2.426537 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 2.426537 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 91.01172 94.35580 88.70792 assigned negative charge : -727.2772 centred at (gu) : 90.96791 94.21600 88.86935 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 231042 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38874 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 108285 mr = 172175 m= 31171 mr = 86365 m= 4952 mr = 23501 m= 348 mr = 3211 m= 8 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 2883 time to turn everything in is 1.200000 number of dielectric boundary points 90387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 37112 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) : 1.617692 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4081963E-02 0.1015018 midg,1,midg; midg,igrid,midg -0.1426369 -0.1455171 1,midg,midg; igrid,midg,midg -0.7291272 3.5432067E-02 gauss-seidel spectral radius is 0.9992210 estimated iterations to convergence 283 setup time was (sec) 1.450000 now iterating at: 08:55:54 rms-change max change #iterations 11.22221 340.2172 at 10iterations 6.564251 169.7321 at 20iterations 3.819098 85.17398 at 30iterations 2.212876 45.92948 at 40iterations 1.274576 27.49105 at 50iterations 0.7350370 15.73047 at 60iterations 0.4218892 9.261105 at 70iterations 0.2415145 4.731270 at 80iterations 0.1379031 2.682236 at 90iterations 7.8911863E-02 1.495416 at 100iterations 4.5080330E-02 0.9941266 at 110iterations 2.5679760E-02 0.4566374 at 120iterations 1.4687782E-02 0.3019047 at 130iterations 8.4099779E-03 0.1453457 at 140iterations 4.8422921E-03 7.8605652E-02 at 150iterations 2.8264236E-03 4.8734665E-02 at 160iterations 1.6926625E-03 2.9190063E-02 at 170iterations 1.0565064E-03 1.7637253E-02 at 180iterations finished qdiffx linear iterations at : 08:56:05 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 1.0565064E-03 1.7637253E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 08:56:07 13.275u 0.224s 0:14.89 90.5% 0+0k 0+0io 0pf+0w