Wed Dec 28 11:02:00 PST 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+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 Wed Dec 28 2011 at 11:02:00 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.5659057 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): -35.12100 10.13600 ymin,ymax (A): 0.9650000 41.45800 zmin,zma (A): -3.703000 59.20500 x,y,z range (A): 45.25700 40.49300 62.90800 scale (grids/A): 0.5659057 object centre (A): -12.49250 21.21150 27.75100 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 2.681005 assigned positive charge : 288.9120 centred at (gu) : 90.48990 89.39786 90.00060 assigned negative charge : -286.2313 centred at (gu) : 90.40755 89.54099 90.00193 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4134 nv = 96 ne = 84 npr = 40406 no. pairs analyzed = 40406 no. exposed pairs = 2410 no. arc points = 17157 no. surface atoms = 832 nbur = 1137 mkacc time = 0.1300000 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 = 1.540000 m= 161 mr = 2178 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1802 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5503575E-10 3.3165476E-10 midg,1,midg; midg,igrid,midg 1.8268932E-09 -8.0668078E-10 1,midg,midg; igrid,midg,midg -3.4217118E-10 1.1922404E-09 gauss-seidel spectral radius is 0.9838064 estimated iterations to convergence 65 setup time was (sec) 0.6000000 now iterating at: 11:02:01 rms-change max change #iterations 6.6428617E-02 17.74773 at 10iterations 4.9171164E-03 0.9467354 at 20iterations 3.6050432E-04 7.1796417E-02 at 30iterations 2.6166488E-05 5.2249432E-03 at 40iterations 1.9057682E-06 3.2663345E-04 at 50iterations finished qdiffx linear iterations at : 11:02:04 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.9057682E-06 3.2663345E-04 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 11:02:06 4.434u 0.457s 0:06.37 76.6% 0+0k 0+0io 5pf+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 Wed Dec 28 2011 at 11:02:06 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.697717 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): -35.12100 10.13600 ymin,ymax (A): 0.9650000 41.45800 zmin,zma (A): -3.703000 59.20500 x,y,z range (A): 45.25700 40.49300 62.90800 scale (grids/A): 1.697717 object centre (A): -12.49250 21.21150 27.75100 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 2.681005 assigned positive charge : 288.9120 centred at (gu) : 91.46996 88.19344 90.00191 assigned negative charge : -286.2313 centred at (gu) : 91.22281 88.62321 90.00606 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 45507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14624 mr = 30863 m= 1657 mr = 10474 m= 48 mr = 886 m= 0 mr = 7 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 19606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14178 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) : 0.5659057 object centre at (A) : -12.49250 21.21150 27.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8447977E-02 1.9026117E-02 midg,1,midg; midg,igrid,midg 2.4376966E-03 -4.7209854E-03 1,midg,midg; igrid,midg,midg -2.7303500E-03 -6.4864830E-04 gauss-seidel spectral radius is 0.9982014 estimated iterations to convergence 187 setup time was (sec) 0.8600000 now iterating at: 11:02:09 rms-change max change #iterations 2.799063 166.3244 at 10iterations 1.163857 51.77328 at 20iterations 0.4860145 20.03612 at 30iterations 0.2040316 9.916204 at 40iterations 8.5007459E-02 3.608509 at 50iterations 3.5585474E-02 1.520500 at 60iterations 1.4902647E-02 0.5901999 at 70iterations 6.2356647E-03 0.2666945 at 80iterations 2.6097475E-03 0.1212361 at 90iterations 1.0962441E-03 4.5627117E-02 at 100iterations 4.5811114E-04 2.1322250E-02 at 110iterations 1.9126636E-04 8.3460808E-03 at 120iterations finished qdiffx linear iterations at : 11:02:21 total time elapsed so far: 13.18000 # loops : 120 mean,max change (kT/e) : 1.9126636E-04 8.3460808E-03 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.41000 DelPhi exited at 11:02:22 13.410u 0.616s 0:15.75 89.0% 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 Wed Dec 28 2011 at 11:02:22 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.546576 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): -35.12100 10.13600 ymin,ymax (A): 0.9650000 41.45800 zmin,zma (A): -3.703000 59.20500 x,y,z range (A): 45.25700 40.49300 62.90800 scale (grids/A): 2.546576 object centre (A): -12.49250 21.21150 27.75100 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 2.681005 assigned positive charge : 288.9120 centred at (gu) : 92.20484 87.29028 90.00282 assigned negative charge : -286.2313 centred at (gu) : 91.83423 87.93481 90.00914 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 105478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 grid for indexing accessible points = 1.400000 m= 50127 mr = 75207 m= 15163 mr = 40462 m= 2689 mr = 11819 m= 194 mr = 1838 m= 5 mr = 104 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 44227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 14687 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) : 1.697717 object centre at (A) : -12.49250 21.21150 27.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1801174 0.1736035 midg,1,midg; midg,igrid,midg 1.6820537E-03 -6.9188550E-02 1,midg,midg; igrid,midg,midg -5.2536752E-02 -3.4051023E-02 gauss-seidel spectral radius is 0.9991087 estimated iterations to convergence 265 setup time was (sec) 1.830000 now iterating at: 11:02:25 rms-change max change #iterations 7.051033 302.1614 at 10iterations 3.872280 121.8350 at 20iterations 2.120128 54.84105 at 30iterations 1.159402 28.30282 at 40iterations 0.6306485 14.91247 at 50iterations 0.3424434 9.043200 at 60iterations 0.1862374 4.877854 at 70iterations 0.1012426 2.243007 at 80iterations 5.4928843E-02 1.385109 at 90iterations 2.9894806E-02 0.7507591 at 100iterations 1.6251354E-02 0.3965185 at 110iterations 8.8235168E-03 0.2014160 at 120iterations 4.7883750E-03 0.1069717 at 130iterations 2.5918337E-03 5.8425903E-02 at 140iterations 1.4091374E-03 3.5103798E-02 at 150iterations 7.6491118E-04 1.8313676E-02 at 160iterations 4.1477539E-04 9.3126297E-03 at 170iterations 2.2526056E-04 5.0921440E-03 at 180iterations finished qdiffx linear iterations at : 11:02:49 total time elapsed so far: 25.84000 # loops : 180 mean,max change (kT/e) : 2.2526056E-04 5.0921440E-03 energy calculations done at 25.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.07000 DelPhi exited at 11:02:49 26.073u 0.751s 0:27.24 98.4% 0+0k 0+0io 0pf+0w