Sat Oct 8 16:38:48 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 Sat Oct 8 2011 at 16:38:49 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4484 !!! WARNING: GLM 204 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5460292 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): 20.38900 79.55300 ymin,ymax (A): 118.2270 183.4250 zmin,zma (A): -1.051000 60.12000 x,y,z range (A): 59.16400 65.19798 61.17100 scale (grids/A): 0.5460292 object centre (A): 49.97100 150.8260 29.53450 number of atom coordinates read : 4484 total number of charged atoms : 4310 net assigned charge : 2.406049 assigned positive charge : 686.2245 centred at (gu) : 90.80293 89.64922 87.48569 assigned negative charge : -683.8220 centred at (gu) : 90.79282 89.58280 87.51072 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8625 nv = 96 ne = 84 npr = 90391 no. pairs analyzed = 90391 no. exposed pairs = 5595 no. arc points = 38554 no. surface atoms = 1873 nbur = 2611 mkacc time = 0.2300000 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 = 1.568000 m= 383 mr = 4577 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4700000 number of dielectric boundary points 4403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4024 ## 537 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 11523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4617357E-10 -5.7422553E-11 midg,1,midg; midg,igrid,midg -5.8674549E-10 7.4409362E-10 1,midg,midg; igrid,midg,midg 3.4397370E-11 2.9957975E-10 gauss-seidel spectral radius is 0.9828201 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 16:38:50 rms-change max change #iterations 9.0939656E-02 11.65489 at 10iterations 6.6340663E-03 0.9452286 at 20iterations 1.0568169E-03 0.1509209 at 30iterations 3.5277166E-04 4.8154831E-02 at 40iterations 1.2951675E-04 1.6565323E-02 at 50iterations finished qdiffx linear iterations at : 16:38:53 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 1.2951675E-04 1.6565323E-02 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 16:38:54 4.705u 0.395s 0:05.44 93.5% 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 Sat Oct 8 2011 at 16:38:54 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4484 !!! WARNING: GLM 204 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.638088 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): 20.38900 79.55300 ymin,ymax (A): 118.2270 183.4250 zmin,zma (A): -1.051000 60.12000 x,y,z range (A): 59.16400 65.19798 61.17100 scale (grids/A): 1.638088 object centre (A): 49.97100 150.8260 29.53450 number of atom coordinates read : 4484 total number of charged atoms : 4310 net assigned charge : 2.406049 assigned positive charge : 686.2245 centred at (gu) : 92.40745 88.94660 82.45605 assigned negative charge : -683.8220 centred at (gu) : 92.37840 88.74795 82.53171 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 96859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30808 mr = 67642 m= 3495 mr = 21021 m= 102 mr = 1790 m= 0 mr = 8 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 409 time to turn everything in is 0.7900000 number of dielectric boundary points 40803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 439 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 33005 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) : 0.5460292 object centre at (A) : 49.97100 150.8260 29.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6824695E-03 8.8623157E-03 midg,1,midg; midg,igrid,midg 1.1229224E-02 3.1611498E-02 1,midg,midg; igrid,midg,midg -2.5165010E-02 -1.3097642E-02 gauss-seidel spectral radius is 0.9983473 estimated iterations to convergence 195 setup time was (sec) 1.090000 now iterating at: 16:38:56 rms-change max change #iterations 4.275165 152.0221 at 10iterations 1.849354 60.14375 at 20iterations 0.8024796 24.20127 at 30iterations 0.3485249 10.93747 at 40iterations 0.1515285 4.406036 at 50iterations 6.5977737E-02 2.015055 at 60iterations 2.8812889E-02 0.9078875 at 70iterations 1.2647895E-02 0.3698082 at 80iterations 5.6270771E-03 0.1635265 at 90iterations 2.5915685E-03 8.6863518E-02 at 100iterations 1.2729500E-03 3.9535522E-02 at 110iterations 6.8783318E-04 2.1581650E-02 at 120iterations finished qdiffx linear iterations at : 16:39:06 total time elapsed so far: 11.41000 # loops : 120 mean,max change (kT/e) : 6.8783318E-04 2.1581650E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 16:39:06 11.578u 0.456s 0:12.30 97.7% 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 Sat Oct 8 2011 at 16:39:06 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4484 !!! WARNING: GLM 204 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.457131 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): 20.38900 79.55300 ymin,ymax (A): 118.2270 183.4250 zmin,zma (A): -1.051000 60.12000 x,y,z range (A): 59.16400 65.19798 61.17100 scale (grids/A): 2.457131 object centre (A): 49.97100 150.8260 29.53450 number of atom coordinates read : 4484 total number of charged atoms : 4310 net assigned charge : 2.406049 assigned positive charge : 686.2245 centred at (gu) : 93.61106 88.41949 78.68393 assigned negative charge : -683.8220 centred at (gu) : 93.56752 88.12191 78.79775 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 224996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106171 mr = 165293 m= 31340 mr = 83916 m= 5661 mr = 23338 m= 450 mr = 3785 m= 15 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 1414 time to turn everything in is 1.990000 number of dielectric boundary points 92079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 34439 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) : 1.638088 object centre at (A) : 49.97100 150.8260 29.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7560853E-02 0.1940808 midg,1,midg; midg,igrid,midg 0.2054156 0.5613404 1,midg,midg; igrid,midg,midg -0.5032171 -0.1980671 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 2.350000 now iterating at: 16:39:09 rms-change max change #iterations 11.02779 298.0505 at 10iterations 6.403587 124.5912 at 20iterations 3.694459 80.76203 at 30iterations 2.127214 41.17570 at 40iterations 1.221236 21.24541 at 50iterations 0.6973750 12.05534 at 60iterations 0.3978671 8.579082 at 70iterations 0.2270001 3.905579 at 80iterations 0.1293186 2.559164 at 90iterations 7.3572680E-02 1.328587 at 100iterations 4.1735251E-02 0.7440066 at 110iterations 2.3789389E-02 0.4203253 at 120iterations 1.3505067E-02 0.2519188 at 130iterations 7.6954435E-03 0.1377234 at 140iterations 4.3957350E-03 7.7907562E-02 at 150iterations 2.5311010E-03 4.6873093E-02 at 160iterations 1.4744059E-03 2.7072906E-02 at 170iterations 8.7671814E-04 1.6070366E-02 at 180iterations finished qdiffx linear iterations at : 16:39:27 total time elapsed so far: 19.89000 # loops : 180 mean,max change (kT/e) : 8.7671814E-04 1.6070366E-02 energy calculations done at 19.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.06000 DelPhi exited at 16:39:27 20.060u 0.486s 0:20.85 98.5% 0+0k 0+0io 0pf+0w