Tue Oct 11 03:21:11 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 Tue Oct 11 2011 at 03:21:11 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 77 has a net charge of -0.4750 !!! WARNING: SEP 223 has a net charge of -0.4750 !!! WARNING: SEP 226 has a net charge of -0.4750 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: 0.5364031 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): -20.47200 38.71600 ymin,ymax (A): 24.22600 75.26600 zmin,zma (A): 70.96900 137.3370 x,y,z range (A): 59.18800 51.04000 66.36800 scale (grids/A): 0.5364031 object centre (A): 9.122002 49.74600 104.1530 number of atom coordinates read : 3214 total number of charged atoms : 3065 net assigned charge : -8.518985 assigned positive charge : 482.0188 centred at (gu) : 88.25950 88.64722 92.68117 assigned negative charge : -490.5388 centred at (gu) : 88.25907 88.68850 92.72930 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5809 nv = 96 ne = 84 npr = 66806 no. pairs analyzed = 66806 no. exposed pairs = 3905 no. arc points = 27480 no. surface atoms = 1317 nbur = 1897 mkacc time = 0.1100000 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= 229 mr = 3019 m= 1 mr = 11 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 0.2300000 number of dielectric boundary points 3009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2864 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7847 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3007148E-11 -1.1722220E-09 midg,1,midg; midg,igrid,midg -1.9986772E-10 -4.0147366E-10 1,midg,midg; igrid,midg,midg -5.4443849E-10 -2.3008906E-10 gauss-seidel spectral radius is 0.9821010 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 03:21:12 rms-change max change #iterations 7.1479850E-02 11.11428 at 10iterations 4.6660462E-03 0.7124939 at 20iterations 3.5219421E-04 6.3039780E-02 at 30iterations 4.7812948E-05 9.2923641E-03 at 40iterations 9.4671104E-06 1.9856095E-03 at 50iterations finished qdiffx linear iterations at : 03:21:14 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 9.4671104E-06 1.9856095E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 03:21:15 3.418u 0.183s 0:03.91 91.8% 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 Tue Oct 11 2011 at 03:21:15 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 77 has a net charge of -0.4750 !!! WARNING: SEP 223 has a net charge of -0.4750 !!! WARNING: SEP 226 has a net charge of -0.4750 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: 1.609209 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): -20.47200 38.71600 ymin,ymax (A): 24.22600 75.26600 zmin,zma (A): 70.96900 137.3370 x,y,z range (A): 59.18800 51.04000 66.36800 scale (grids/A): 1.609209 object centre (A): 9.122002 49.74600 104.1530 number of atom coordinates read : 3214 total number of charged atoms : 3065 net assigned charge : -8.518985 assigned positive charge : 482.0188 centred at (gu) : 84.77745 85.94096 98.04253 assigned negative charge : -490.5388 centred at (gu) : 84.77674 86.06511 98.18751 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19902 mr = 44026 m= 1992 mr = 13845 m= 53 mr = 1035 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.3300000 number of dielectric boundary points 27818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 369 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 23347 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) : 0.5364031 object centre at (A) : 9.122002 49.74600 104.1530 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3187133E-02 -1.4778617E-02 midg,1,midg; midg,igrid,midg -6.2786406E-03 -6.3786609E-03 1,midg,midg; igrid,midg,midg 1.2346507E-03 -4.3326602E-03 gauss-seidel spectral radius is 0.9981388 estimated iterations to convergence 184 setup time was (sec) 0.5500000 now iterating at: 03:21:16 rms-change max change #iterations 3.351750 159.5872 at 10iterations 1.385926 54.51793 at 20iterations 0.5715021 21.00067 at 30iterations 0.2357868 8.749604 at 40iterations 9.7433433E-02 4.458513 at 50iterations 4.0097665E-02 1.310735 at 60iterations 1.6577806E-02 0.6657715 at 70iterations 6.8721264E-03 0.2448983 at 80iterations 2.8440279E-03 0.1032562 at 90iterations 1.1865644E-03 4.1675568E-02 at 100iterations 5.0009263E-04 1.7524719E-02 at 110iterations 2.1247561E-04 7.6761246E-03 at 120iterations finished qdiffx linear iterations at : 03:21:23 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.1247561E-04 7.6761246E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 03:21:23 7.844u 0.218s 0:08.51 94.5% 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 Tue Oct 11 2011 at 03:21:23 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 77 has a net charge of -0.4750 !!! WARNING: SEP 223 has a net charge of -0.4750 !!! WARNING: SEP 226 has a net charge of -0.4750 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: 2.413814 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): -20.47200 38.71600 ymin,ymax (A): 24.22600 75.26600 zmin,zma (A): 70.96900 137.3370 x,y,z range (A): 59.18800 51.04000 66.36800 scale (grids/A): 2.413814 object centre (A): 9.122002 49.74600 104.1530 number of atom coordinates read : 3214 total number of charged atoms : 3065 net assigned charge : -8.518985 assigned positive charge : 482.0188 centred at (gu) : 82.16596 83.91108 102.0636 assigned negative charge : -490.5388 centred at (gu) : 82.16516 84.09756 102.2811 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 69191 mr = 107664 m= 19641 mr = 55095 m= 3202 mr = 14827 m= 194 mr = 2167 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 487 time to turn everything in is 0.7900000 number of dielectric boundary points 62885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24475 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) : 1.609209 object centre at (A) : 9.122002 49.74600 104.1530 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4057215 -0.3304830 midg,1,midg; midg,igrid,midg -8.1789613E-02 -9.6451268E-02 1,midg,midg; igrid,midg,midg 0.1229655 -6.0200715E-03 gauss-seidel spectral radius is 0.9991244 estimated iterations to convergence 267 setup time was (sec) 1.050000 now iterating at: 03:21:25 rms-change max change #iterations 8.829952 289.1901 at 10iterations 4.924839 117.3248 at 20iterations 2.731998 62.13749 at 30iterations 1.511002 35.56148 at 40iterations 0.8320876 18.52454 at 50iterations 0.4563532 10.12764 at 60iterations 0.2508571 5.176333 at 70iterations 0.1377332 3.051075 at 80iterations 7.5306594E-02 1.551572 at 90iterations 4.1369259E-02 0.8934422 at 100iterations 2.2641802E-02 0.4947858 at 110iterations 1.2403065E-02 0.2493248 at 120iterations 6.7907595E-03 0.1414802 at 130iterations 3.7332103E-03 7.7184677E-02 at 140iterations 2.0446109E-03 4.0548325E-02 at 150iterations 1.1259369E-03 2.3172379E-02 at 160iterations 6.2353443E-04 1.2294769E-02 at 170iterations 3.4692226E-04 7.5378418E-03 at 180iterations finished qdiffx linear iterations at : 03:21:36 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 3.4692226E-04 7.5378418E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 03:21:37 12.424u 0.183s 0:13.03 96.6% 0+0k 0+0io 0pf+0w