Mon Nov 8 21:24:36 PST 2010 #!/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.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 Mon Nov 8 2010 at 21:24:36 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.4994389 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 0.4994389 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 91.30943 94.90833 89.22078 assigned negative charge : -408.5823 centred at (gu) : 91.26785 94.98487 89.87395 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4846 nv = 96 ne = 84 npr = 58824 no. pairs analyzed = 58824 no. exposed pairs = 4209 no. arc points = 29977 no. surface atoms = 1416 nbur = 1544 mkacc time = 9.9999994E-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 = 1.680000 m= 166 mr = 2077 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2804 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 6272 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4459516E-10 -4.4266119E-10 midg,1,midg; midg,igrid,midg 4.0604669E-11 2.3541613E-11 1,midg,midg; igrid,midg,midg 3.0094389E-11 1.6244008E-10 gauss-seidel spectral radius is 0.9793878 estimated iterations to convergence 58 setup time was (sec) 0.4100000 now iterating at: 21:24:36 rms-change max change #iterations 4.2150363E-02 10.09555 at 10iterations 2.2549555E-03 0.4028597 at 20iterations 1.8097211E-04 3.6594391E-02 at 30iterations 3.4886478E-05 6.8627596E-03 at 40iterations 8.3450650E-06 1.5599728E-03 at 50iterations finished qdiffx linear iterations at : 21:24:39 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 8.3450650E-06 1.5599728E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 21:24:40 3.437u 0.171s 0:04.07 88.4% 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 Nov 8 2010 at 21:24:40 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.498317 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 1.498317 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 93.92752 104.7242 87.66168 assigned negative charge : -408.5823 centred at (gu) : 93.80348 104.9542 89.62164 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 53497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29977 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 13885 mr = 32566 m= 1155 mr = 8262 m= 17 mr = 414 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 27312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 21114 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) : 0.4994389 object centre at (A) : 14.42550 -19.78950 55.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9527945E-02 -2.6940107E-02 midg,1,midg; midg,igrid,midg 1.9332909E-03 5.3572170E-03 1,midg,midg; igrid,midg,midg -5.6570972E-04 1.6890618E-03 gauss-seidel spectral radius is 0.9978015 estimated iterations to convergence 170 setup time was (sec) 0.5100000 now iterating at: 21:24:41 rms-change max change #iterations 2.563918 161.5743 at 10iterations 0.9655496 44.68100 at 20iterations 0.3657597 16.94829 at 30iterations 0.1396077 5.997722 at 40iterations 5.3025045E-02 2.104734 at 50iterations 2.0108772E-02 0.8983991 at 60iterations 7.7043129E-03 0.3097000 at 70iterations 2.9318088E-03 0.1180878 at 80iterations 1.1208704E-03 4.9676180E-02 at 90iterations 4.3489336E-04 1.7427444E-02 at 100iterations 1.6987012E-04 6.9808960E-03 at 110iterations 6.8316032E-05 2.9811859E-03 at 120iterations finished qdiffx linear iterations at : 21:24:48 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 6.8316032E-05 2.9811859E-03 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 21:24:48 7.742u 0.276s 0:08.50 94.2% 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 Nov 8 2010 at 21:24:49 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 ! Automatically converted from prot.table.ambcrg.ambH by pro # of charge parameter records: 1051 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.247475 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): -9.632999 38.48400 ymin,ymax (A): -52.31200 12.73300 zmin,zma (A): 20.09300 91.37300 x,y,z range (A): 48.11700 65.04500 71.28000 scale (grids/A): 2.247475 object centre (A): 14.42550 -19.78950 55.73300 number of atom coordinates read : 2960 total number of charged atoms : 2825 net assigned charge : 9.500021 assigned positive charge : 418.0813 centred at (gu) : 95.89114 112.0861 86.49230 assigned negative charge : -408.5823 centred at (gu) : 95.70511 112.4313 89.43230 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 124285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29977 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 49730 mr = 81198 m= 12112 mr = 36083 m= 1542 mr = 8037 m= 74 mr = 860 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 61552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22533 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) : 1.498317 object centre at (A) : 14.42550 -19.78950 55.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.085070 -0.4936619 midg,1,midg; midg,igrid,midg 2.5758816E-02 2.9633477E-02 1,midg,midg; igrid,midg,midg -4.4188630E-03 1.3899939E-02 gauss-seidel spectral radius is 0.9989784 estimated iterations to convergence 247 setup time was (sec) 0.9100000 now iterating at: 21:24:50 rms-change max change #iterations 7.104957 210.0244 at 10iterations 3.812173 101.0994 at 20iterations 2.022488 54.13480 at 30iterations 1.067003 30.69145 at 40iterations 0.5604544 14.63005 at 50iterations 0.2944716 8.494232 at 60iterations 0.1539435 3.934605 at 70iterations 8.0713786E-02 2.131287 at 80iterations 4.2071041E-02 0.9943094 at 90iterations 2.1941027E-02 0.5020180 at 100iterations 1.1472534E-02 0.2990713 at 110iterations 5.9774937E-03 0.1883211 at 120iterations 3.1000462E-03 7.4024200E-02 at 130iterations 1.6196137E-03 4.0284377E-02 at 140iterations 8.4379286E-04 2.1490455E-02 at 150iterations 4.4028569E-04 1.0211706E-02 at 160iterations 2.2962494E-04 6.1111450E-03 at 170iterations 1.2003473E-04 3.0393600E-03 at 180iterations finished qdiffx linear iterations at : 21:25:01 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 1.2003473E-04 3.0393600E-03 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 21:25:02 12.308u 0.423s 0:13.43 94.7% 0+0k 0+0io 0pf+0w