Sun Oct 9 07:57:29 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 Sun Oct 9 2011 at 07:57:29 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2280 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.5392632 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): 4.671000 50.10900 ymin,ymax (A): -24.74300 41.27300 zmin,zma (A): -19.50800 30.29200 x,y,z range (A): 45.43800 66.01600 49.80000 scale (grids/A): 0.5392632 object centre (A): 27.39000 8.264999 5.392000 number of atom coordinates read : 2280 total number of charged atoms : 2090 net assigned charge : -3.499990 assigned positive charge : 340.7554 centred at (gu) : 89.84904 87.46844 90.08729 assigned negative charge : -344.2557 centred at (gu) : 89.82485 87.70652 90.14163 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4314 nv = 96 ne = 84 npr = 45279 no. pairs analyzed = 45279 no. exposed pairs = 3030 no. arc points = 21947 no. surface atoms = 1015 nbur = 1265 mkacc time = 7.9999998E-02 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= 154 mr = 2087 m= 0 mr = 4 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2210 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2474897E-11 -4.1675560E-10 midg,1,midg; midg,igrid,midg 1.4036557E-09 -6.1895000E-10 1,midg,midg; igrid,midg,midg -2.9797478E-10 -9.1891723E-11 gauss-seidel spectral radius is 0.9822249 estimated iterations to convergence 62 setup time was (sec) 0.3500000 now iterating at: 07:57:29 rms-change max change #iterations 6.0419261E-02 14.07921 at 10iterations 3.8983992E-03 0.7225914 at 20iterations 2.4371079E-04 5.5023193E-02 at 30iterations 1.5446698E-05 2.8243065E-03 at 40iterations 1.0103498E-06 1.7929077E-04 at 50iterations finished qdiffx linear iterations at : 07:57:32 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.0103498E-06 1.7929077E-04 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:57:32 3.324u 0.162s 0:03.75 92.8% 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 Sun Oct 9 2011 at 07:57:32 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2280 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 1.617790 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): 4.671000 50.10900 ymin,ymax (A): -24.74300 41.27300 zmin,zma (A): -19.50800 30.29200 x,y,z range (A): 45.43800 66.01600 49.80000 scale (grids/A): 1.617790 object centre (A): 27.39000 8.264999 5.392000 number of atom coordinates read : 2280 total number of charged atoms : 2090 net assigned charge : -3.499990 assigned positive charge : 340.7554 centred at (gu) : 89.54685 82.40473 90.26122 assigned negative charge : -344.2557 centred at (gu) : 89.47427 83.11937 90.42472 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21947 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14113 mr = 30863 m= 1426 mr = 9525 m= 35 mr = 645 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 241 time to turn everything in is 0.2400000 number of dielectric boundary points 22201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 15972 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) : 0.5392632 object centre at (A) : 27.39000 8.264999 5.392000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4245605E-04 -3.6252548E-03 midg,1,midg; midg,igrid,midg 1.8064454E-02 -1.5190365E-02 1,midg,midg; igrid,midg,midg -2.3206789E-04 -6.9765644E-03 gauss-seidel spectral radius is 0.9980731 estimated iterations to convergence 181 setup time was (sec) 0.4400000 now iterating at: 07:57:33 rms-change max change #iterations 2.832325 243.3268 at 10iterations 1.144266 67.78970 at 20iterations 0.4634990 26.11247 at 30iterations 0.1875686 8.981581 at 40iterations 7.5779721E-02 3.545868 at 50iterations 3.0718299E-02 1.407954 at 60iterations 1.2494696E-02 0.5359344 at 70iterations 5.0510126E-03 0.2101647 at 80iterations 2.0471204E-03 9.0871811E-02 at 90iterations 8.3518447E-04 3.2608032E-02 at 100iterations 3.3771520E-04 1.4698029E-02 at 110iterations 1.3706870E-04 5.7220459E-03 at 120iterations finished qdiffx linear iterations at : 07:57:40 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.3706870E-04 5.7220459E-03 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 07:57:40 7.416u 0.207s 0:07.94 95.8% 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 Sun Oct 9 2011 at 07:57:40 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2280 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.426684 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): 4.671000 50.10900 ymin,ymax (A): -24.74300 41.27300 zmin,zma (A): -19.50800 30.29200 x,y,z range (A): 45.43800 66.01600 49.80000 scale (grids/A): 2.426684 object centre (A): 27.39000 8.264999 5.392000 number of atom coordinates read : 2280 total number of charged atoms : 2090 net assigned charge : -3.499990 assigned positive charge : 340.7554 centred at (gu) : 89.32027 78.60690 90.39182 assigned negative charge : -344.2557 centred at (gu) : 89.21143 79.67895 90.63708 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 110503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21947 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 49305 mr = 75943 m= 13564 mr = 38352 m= 2206 mr = 10017 m= 151 mr = 1397 m= 0 mr = 57 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 0.5900000 number of dielectric boundary points 49963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 16698 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) : 1.617790 object centre at (A) : 27.39000 8.264999 5.392000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5175747E-02 -3.7853099E-02 midg,1,midg; midg,igrid,midg 0.7096752 -0.2400418 1,midg,midg; igrid,midg,midg 2.1941232E-02 -0.1222268 gauss-seidel spectral radius is 0.9990850 estimated iterations to convergence 261 setup time was (sec) 0.8200000 now iterating at: 07:57:41 rms-change max change #iterations 7.550921 362.6331 at 10iterations 4.150952 159.7576 at 20iterations 2.294355 73.18117 at 30iterations 1.248039 42.61696 at 40iterations 0.6814167 19.84416 at 50iterations 0.3701802 9.370289 at 60iterations 0.2002765 5.122190 at 70iterations 0.1083994 2.846484 at 80iterations 5.8597758E-02 1.544162 at 90iterations 3.1652253E-02 0.8168488 at 100iterations 1.7122610E-02 0.4268589 at 110iterations 9.2388382E-03 0.2326453 at 120iterations 4.9714805E-03 0.1144948 at 130iterations 2.6856952E-03 7.7285767E-02 at 140iterations 1.4491382E-03 3.7166774E-02 at 150iterations 7.8253221E-04 1.8096924E-02 at 160iterations 4.2062619E-04 1.0480881E-02 at 170iterations 2.2662936E-04 5.6238174E-03 at 180iterations finished qdiffx linear iterations at : 07:57:52 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 2.2662936E-04 5.6238174E-03 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 07:57:53 11.659u 0.187s 0:12.10 97.7% 0+0k 0+0io 0pf+0w