Mon Oct 10 14:11:58 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 14:11:58 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2039 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: ASP 175 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6706225 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): 7.138000 60.22300 ymin,ymax (A): 2.388000 50.05400 zmin,zma (A): 12.49000 55.81800 x,y,z range (A): 53.08500 47.66600 43.32800 scale (grids/A): 0.6706225 object centre (A): 33.68050 26.22100 34.15400 number of atom coordinates read : 2039 total number of charged atoms : 1900 net assigned charge : 3.648003 assigned positive charge : 307.7127 centred at (gu) : 87.67784 89.40000 89.78492 assigned negative charge : -304.0648 centred at (gu) : 87.82330 89.42766 89.83598 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6167 nv = 96 ne = 84 npr = 41437 no. pairs analyzed = 41437 no. exposed pairs = 2524 no. arc points = 17787 no. surface atoms = 854 nbur = 1185 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3388 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1648 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7075 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2637298E-08 1.0677719E-09 midg,1,midg; midg,igrid,midg 1.9176161E-08 5.2322910E-09 1,midg,midg; igrid,midg,midg 6.5448013E-08 -1.1139773E-08 gauss-seidel spectral radius is 0.9884216 estimated iterations to convergence 76 setup time was (sec) 0.5300000 now iterating at: 14:11:59 rms-change max change #iterations 0.1559984 22.31270 at 10iterations 1.7443722E-02 2.786441 at 20iterations 1.8896927E-03 0.2853420 at 30iterations 2.2654743E-04 3.3117294E-02 at 40iterations 3.5263816E-05 6.1225891E-03 at 50iterations finished qdiffx linear iterations at : 14:12:03 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 3.5263816E-05 6.1225891E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 14:12:03 4.134u 0.214s 0:04.69 92.5% 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 14:12:03 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2039 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: ASP 175 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.011868 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): 7.138000 60.22300 ymin,ymax (A): 2.388000 50.05400 zmin,zma (A): 12.49000 55.81800 x,y,z range (A): 53.08500 47.66600 43.32800 scale (grids/A): 2.011868 object centre (A): 33.68050 26.22100 34.15400 number of atom coordinates read : 2039 total number of charged atoms : 1900 net assigned charge : 3.648003 assigned positive charge : 307.7127 centred at (gu) : 83.03323 88.19968 89.35482 assigned negative charge : -304.0648 centred at (gu) : 83.46965 88.28287 89.50768 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 24145 mr = 45681 m= 4247 mr = 17670 m= 341 mr = 2718 m= 7 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 28635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15011 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) : 0.6706225 object centre at (A) : 33.68050 26.22100 34.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6171567E-02 4.0863156E-03 midg,1,midg; midg,igrid,midg 3.4479126E-02 1.2361716E-02 1,midg,midg; igrid,midg,midg -2.8962927E-02 -4.7907304E-02 gauss-seidel spectral radius is 0.9987112 estimated iterations to convergence 221 setup time was (sec) 0.8400000 now iterating at: 14:12:04 rms-change max change #iterations 4.180202 215.6640 at 10iterations 1.996278 68.65746 at 20iterations 0.9495918 31.68822 at 30iterations 0.4572621 16.04914 at 40iterations 0.2188331 7.279882 at 50iterations 0.1048276 3.438784 at 60iterations 5.0129026E-02 1.585337 at 70iterations 2.3907959E-02 0.8059425 at 80iterations 1.1450589E-02 0.3810139 at 90iterations 5.5048144E-03 0.2000065 at 100iterations 2.6331709E-03 8.6577415E-02 at 110iterations 1.2592060E-03 4.2455673E-02 at 120iterations finished qdiffx linear iterations at : 14:12:13 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.2592060E-03 4.2455673E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 14:12:13 9.403u 0.263s 0:10.10 95.6% 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 14:12:13 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2039 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: ASP 175 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.017802 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): 7.138000 60.22300 ymin,ymax (A): 2.388000 50.05400 zmin,zma (A): 12.49000 55.81800 x,y,z range (A): 53.08500 47.66600 43.32800 scale (grids/A): 3.017802 object centre (A): 33.68050 26.22100 34.15400 number of atom coordinates read : 2039 total number of charged atoms : 1900 net assigned charge : 3.648003 assigned positive charge : 307.7127 centred at (gu) : 79.54984 87.29952 89.03217 assigned negative charge : -304.0648 centred at (gu) : 80.20451 87.42421 89.26154 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 153107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 76984 mr = 110963 m= 28938 mr = 62799 m= 7928 mr = 23218 m= 1357 mr = 5883 m= 83 mr = 913 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 64595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 15200 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) : 2.011868 object centre at (A) : 33.68050 26.22100 34.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2711379 2.4243653E-02 midg,1,midg; midg,igrid,midg 0.2493136 1.9431198E-02 1,midg,midg; igrid,midg,midg -0.4883601 -0.5964561 gauss-seidel spectral radius is 0.9992691 estimated iterations to convergence 292 setup time was (sec) 1.830000 now iterating at: 14:12:15 rms-change max change #iterations 9.660352 369.8104 at 10iterations 5.670990 129.3676 at 20iterations 3.310175 75.35458 at 30iterations 1.929309 47.15350 at 40iterations 1.121127 24.28797 at 50iterations 0.6528414 13.75762 at 60iterations 0.3783270 7.877460 at 70iterations 0.2187429 4.381887 at 80iterations 0.1267352 2.486708 at 90iterations 7.3202513E-02 1.414486 at 100iterations 4.2480305E-02 0.7772102 at 110iterations 2.4406092E-02 0.4703789 at 120iterations 1.4136781E-02 0.2716370 at 130iterations 8.1539173E-03 0.1663742 at 140iterations 4.7199754E-03 9.1941833E-02 at 150iterations 2.7281919E-03 4.7729492E-02 at 160iterations 1.5810620E-03 3.0754566E-02 at 170iterations 9.1630069E-04 1.9634247E-02 at 180iterations finished qdiffx linear iterations at : 14:12:29 total time elapsed so far: 15.70000 # loops : 180 mean,max change (kT/e) : 9.1630069E-04 1.9634247E-02 energy calculations done at 15.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.88000 DelPhi exited at 14:12:30 15.879u 0.344s 0:16.59 97.7% 0+0k 0+0io 0pf+0w