Mon Oct 10 13:59:31 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 13:59:31 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 0.5049145 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): -3.394000 67.11300 ymin,ymax (A): -12.35100 38.34800 zmin,zma (A): -20.07200 45.26700 x,y,z range (A): 70.50700 50.69901 65.33900 scale (grids/A): 0.5049145 object centre (A): 31.85950 12.99850 12.59750 number of atom coordinates read : 4432 total number of charged atoms : 4277 net assigned charge : -4.985955 assigned positive charge : 673.5210 centred at (gu) : 88.04093 89.88490 90.80696 assigned negative charge : -678.5092 centred at (gu) : 88.11369 90.00647 90.83368 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6964 nv = 96 ne = 84 npr = 93316 no. pairs analyzed = 93316 no. exposed pairs = 5030 no. arc points = 33876 no. surface atoms = 1722 nbur = 2710 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 = 1.680000 m= 243 mr = 3856 m= 0 mr = 10 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3000000 number of dielectric boundary points 3341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3418 ## 514 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3296664E-12 -1.3454914E-10 midg,1,midg; midg,igrid,midg 1.7766752E-10 -2.8518293E-10 1,midg,midg; igrid,midg,midg 1.4055569E-10 -1.1804614E-10 gauss-seidel spectral radius is 0.9799065 estimated iterations to convergence 58 setup time was (sec) 0.4900000 now iterating at: 13:59:32 rms-change max change #iterations 6.3103475E-02 10.20970 at 10iterations 3.5030651E-03 0.5638671 at 20iterations 3.7218787E-04 5.5545807E-02 at 30iterations 8.7858993E-05 1.2755752E-02 at 40iterations 2.3616802E-05 3.5920143E-03 at 50iterations finished qdiffx linear iterations at : 13:59:35 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 2.3616802E-05 3.5920143E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 13:59:36 3.576u 0.195s 0:04.70 80.0% 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 Mon Oct 10 2011 at 13:59:36 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 1.514743 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): -3.394000 67.11300 ymin,ymax (A): -12.35100 38.34800 zmin,zma (A): -20.07200 45.26700 x,y,z range (A): 70.50700 50.69901 65.33900 scale (grids/A): 1.514743 object centre (A): 31.85950 12.99850 12.59750 number of atom coordinates read : 4432 total number of charged atoms : 4277 net assigned charge : -4.985955 assigned positive charge : 673.5210 centred at (gu) : 84.12184 89.65376 92.41975 assigned negative charge : -678.5092 centred at (gu) : 84.34064 90.01899 92.50044 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 79981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33876 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23646 mr = 57340 m= 2100 mr = 16381 m= 30 mr = 976 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 897 time to turn everything in is 0.4000000 number of dielectric boundary points 31060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 32026 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) : 0.5049145 object centre at (A) : 31.85950 12.99850 12.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2244381E-03 -1.0143218E-02 midg,1,midg; midg,igrid,midg 3.2952246E-03 -1.0237487E-02 1,midg,midg; igrid,midg,midg 1.4355392E-02 -3.6748894E-03 gauss-seidel spectral radius is 0.9980064 estimated iterations to convergence 178 setup time was (sec) 0.6200000 now iterating at: 13:59:37 rms-change max change #iterations 3.563423 159.7847 at 10iterations 1.424511 49.70984 at 20iterations 0.5701985 18.24150 at 30iterations 0.2291893 7.500307 at 40iterations 9.1744073E-02 3.192118 at 50iterations 3.6932472E-02 1.193422 at 60iterations 1.4890470E-02 0.4681702 at 70iterations 6.0310299E-03 0.1971436 at 80iterations 2.4833451E-03 7.7104568E-02 at 90iterations 1.0569239E-03 3.7689209E-02 at 100iterations 4.7741894E-04 1.6608238E-02 at 110iterations 2.3756732E-04 8.4991455E-03 at 120iterations finished qdiffx linear iterations at : 13:59:44 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.3756732E-04 8.4991455E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:59:45 7.940u 0.215s 0:08.75 93.1% 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 13:59:46 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 2.272115 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): -3.394000 67.11300 ymin,ymax (A): -12.35100 38.34800 zmin,zma (A): -20.07200 45.26700 x,y,z range (A): 70.50700 50.69901 65.33900 scale (grids/A): 2.272115 object centre (A): 31.85950 12.99850 12.59750 number of atom coordinates read : 4432 total number of charged atoms : 4277 net assigned charge : -4.985955 assigned positive charge : 673.5210 centred at (gu) : 81.18243 89.48055 93.62914 assigned negative charge : -678.5092 centred at (gu) : 81.51087 90.02844 93.75052 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 186833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33876 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85254 mr = 140348 m= 21701 mr = 68441 m= 2990 mr = 16096 m= 116 mr = 1921 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2875 time to turn everything in is 0.9500000 number of dielectric boundary points 70078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 34125 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) : 1.514743 object centre at (A) : 31.85950 12.99850 12.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2510135 -0.2324226 midg,1,midg; midg,igrid,midg 3.9442033E-02 -0.1665466 1,midg,midg; igrid,midg,midg 0.3514720 -0.3765677 gauss-seidel spectral radius is 0.9991056 estimated iterations to convergence 264 setup time was (sec) 1.190000 now iterating at: 13:59:47 rms-change max change #iterations 9.591856 320.1649 at 10iterations 5.346947 111.2012 at 20iterations 2.962547 60.32880 at 30iterations 1.635206 33.75119 at 40iterations 0.8955193 17.83300 at 50iterations 0.4911462 10.31871 at 60iterations 0.2687378 5.834028 at 70iterations 0.1467969 3.230919 at 80iterations 8.0023430E-02 1.646597 at 90iterations 4.3590028E-02 0.8285170 at 100iterations 2.3806807E-02 0.4710064 at 110iterations 1.2984555E-02 0.2297144 at 120iterations 7.0784711E-03 0.1390953 at 130iterations 3.8512610E-03 7.4696541E-02 at 140iterations 2.1078903E-03 4.2706013E-02 at 150iterations 1.1556164E-03 2.1665573E-02 at 160iterations 6.3752057E-04 1.2668610E-02 at 170iterations 3.5616691E-04 6.5259933E-03 at 180iterations finished qdiffx linear iterations at : 14:00:00 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 3.5616691E-04 6.5259933E-03 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 14:00:00 13.575u 0.225s 0:14.19 97.1% 0+0k 0+0io 0pf+0w