Sat Oct 8 19:25:13 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 19:25:13 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2062 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 614 has a net charge of 1.4000 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: 0.7093188 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): -28.70500 17.61600 ymin,ymax (A): -23.85300 22.88000 zmin,zma (A): -12.34800 37.84100 x,y,z range (A): 46.32100 46.73300 50.18900 scale (grids/A): 0.7093188 object centre (A): -5.544500 -0.4864998 12.74650 number of atom coordinates read : 2062 total number of charged atoms : 1924 net assigned charge : 3.500006 assigned positive charge : 303.4400 centred at (gu) : 89.18192 88.75276 90.30309 assigned negative charge : -299.9403 centred at (gu) : 89.12210 88.94310 90.09721 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7257 nv = 96 ne = 84 npr = 42942 no. pairs analyzed = 42942 no. exposed pairs = 2449 no. arc points = 17586 no. surface atoms = 825 nbur = 1237 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 500 mr = 4218 m= 6 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2500000 number of dielectric boundary points 3461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1444 ## 106 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7824 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9917057E-08 1.3741827E-07 midg,1,midg; midg,igrid,midg 1.5619945E-07 -5.1489334E-08 1,midg,midg; igrid,midg,midg -5.2830101E-10 5.0472167E-08 gauss-seidel spectral radius is 0.9896435 estimated iterations to convergence 80 setup time was (sec) 0.4700000 now iterating at: 19:25:13 rms-change max change #iterations 0.2096345 29.68417 at 10iterations 2.5547341E-02 3.154032 at 20iterations 3.1702486E-03 0.4379807 at 30iterations 3.8846073E-04 6.3835144E-02 at 40iterations 4.8562761E-05 6.2789917E-03 at 50iterations finished qdiffx linear iterations at : 19:25:16 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 4.8562761E-05 6.2789917E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 19:25:16 3.085u 0.152s 0:03.50 92.2% 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 Sat Oct 8 2011 at 19:25:16 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2062 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 614 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.127956 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): -28.70500 17.61600 ymin,ymax (A): -23.85300 22.88000 zmin,zma (A): -12.34800 37.84100 x,y,z range (A): 46.32100 46.73300 50.18900 scale (grids/A): 2.127956 object centre (A): -5.544500 -0.4864998 12.74650 number of atom coordinates read : 2062 total number of charged atoms : 1924 net assigned charge : 3.500006 assigned positive charge : 303.4400 centred at (gu) : 87.54557 86.25827 90.90952 assigned negative charge : -299.9403 centred at (gu) : 87.36649 86.82948 90.29195 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17586 grid for indexing accessible points = 1.400000 m= 30189 mr = 54118 m= 6097 mr = 23072 m= 556 mr = 4068 m= 11 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 655 time to turn everything in is 0.5500000 number of dielectric boundary points 31856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15290 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) : 0.7093188 object centre at (A) : -5.544500 -0.4864998 12.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5765190E-02 1.9407120E-02 midg,1,midg; midg,igrid,midg 3.9987769E-02 9.7676580E-05 1,midg,midg; igrid,midg,midg 1.2371737E-02 4.2896565E-02 gauss-seidel spectral radius is 0.9988419 estimated iterations to convergence 233 setup time was (sec) 0.8100000 now iterating at: 19:25:17 rms-change max change #iterations 4.640157 173.9503 at 10iterations 2.308670 73.39191 at 20iterations 1.155288 38.36553 at 30iterations 0.5765853 16.76482 at 40iterations 0.2880141 8.171931 at 50iterations 0.1438854 4.871024 at 60iterations 7.1779355E-02 2.224685 at 70iterations 3.5676528E-02 1.092915 at 80iterations 1.7760102E-02 0.5675030 at 90iterations 8.8344468E-03 0.2534199 at 100iterations 4.4200015E-03 0.1329517 at 110iterations 2.2058059E-03 6.7131042E-02 at 120iterations finished qdiffx linear iterations at : 19:25:23 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 2.2058059E-03 6.7131042E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 19:25:24 6.925u 0.155s 0:07.35 96.1% 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 Sat Oct 8 2011 at 19:25:24 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2062 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 614 has a net charge of 1.4000 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: 3.191935 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): -28.70500 17.61600 ymin,ymax (A): -23.85300 22.88000 zmin,zma (A): -12.34800 37.84100 x,y,z range (A): 46.32100 46.73300 50.18900 scale (grids/A): 3.191935 object centre (A): -5.544500 -0.4864998 12.74650 number of atom coordinates read : 2062 total number of charged atoms : 1924 net assigned charge : 3.500006 assigned positive charge : 303.4400 centred at (gu) : 86.31843 84.38738 91.36421 assigned negative charge : -299.9403 centred at (gu) : 86.04983 85.24425 90.43794 start vw surface at 0.1300000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 176319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17586 grid for indexing accessible points = 1.400000 m= 94177 mr = 129988 m= 38400 mr = 78871 m= 11457 mr = 31561 m= 2308 mr = 8938 m= 262 mr = 1625 m= 9 mr = 169 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8199999 no. cavity mid-points inaccessible to solvent = 2166 time to turn everything in is 1.680000 number of dielectric boundary points 71775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 15392 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) : 2.127956 object centre at (A) : -5.544500 -0.4864998 12.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1862306 0.2055482 midg,1,midg; midg,igrid,midg 0.3063371 -7.8719050E-02 1,midg,midg; igrid,midg,midg -5.6825811E-03 0.4043223 gauss-seidel spectral radius is 0.9993049 estimated iterations to convergence 299 setup time was (sec) 1.950000 now iterating at: 19:25:26 rms-change max change #iterations 10.07365 442.4230 at 10iterations 5.910572 125.5880 at 20iterations 3.459723 68.57639 at 30iterations 2.026861 37.64318 at 40iterations 1.188672 21.11711 at 50iterations 0.6928530 12.09069 at 60iterations 0.4051001 8.486058 at 70iterations 0.2369646 4.087056 at 80iterations 0.1388528 2.681507 at 90iterations 8.0923997E-02 1.542904 at 100iterations 4.7282554E-02 0.9253311 at 110iterations 2.7691454E-02 0.4663496 at 120iterations 1.6165422E-02 0.2646756 at 130iterations 9.4691971E-03 0.1551323 at 140iterations 5.5274605E-03 0.1071048 at 150iterations 3.2282034E-03 5.5875778E-02 at 160iterations 1.8861513E-03 3.0786514E-02 at 170iterations 1.1035550E-03 1.9081116E-02 at 180iterations finished qdiffx linear iterations at : 19:25:35 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.1035550E-03 1.9081116E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 19:25:36 11.606u 0.193s 0:12.06 97.7% 0+0k 0+0io 0pf+0w