Mon Oct 10 14:41:46 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+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 Oct 10 2011 at 14:41:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 0.6100591 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): -8.526000 46.05800 ymin,ymax (A): -25.30500 33.05000 zmin,zma (A): 9.131000 64.27900 x,y,z range (A): 54.58400 58.35500 55.14800 scale (grids/A): 0.6100591 object centre (A): 18.76600 3.872499 36.70500 number of atom coordinates read : 2461 total number of charged atoms : 2316 net assigned charge : -1.999992 assigned positive charge : 362.6572 centred at (gu) : 89.42687 90.81208 89.17639 assigned negative charge : -364.6577 centred at (gu) : 89.27367 90.68693 89.16907 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6042 nv = 96 ne = 84 npr = 49589 no. pairs analyzed = 49589 no. exposed pairs = 3249 no. arc points = 22789 no. surface atoms = 1094 nbur = 1367 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 259 mr = 3105 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2227 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7454 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8170536E-09 -7.0200956E-10 midg,1,midg; midg,igrid,midg -5.8994201E-09 5.5111191E-09 1,midg,midg; igrid,midg,midg -9.6012318E-09 5.1120317E-09 gauss-seidel spectral radius is 0.9860803 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 14:41:47 rms-change max change #iterations 0.1098347 15.32637 at 10iterations 9.5297210E-03 1.322693 at 20iterations 8.4657158E-04 0.1184540 at 30iterations 7.4262149E-05 1.3729095E-02 at 40iterations 6.6623438E-06 1.0118484E-03 at 50iterations finished qdiffx linear iterations at : 14:41:51 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 6.6623438E-06 1.0118484E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 14:41:51 4.550u 0.397s 0:05.28 93.5% 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 Mon Oct 10 2011 at 14:41:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 1.830177 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): -8.526000 46.05800 ymin,ymax (A): -25.30500 33.05000 zmin,zma (A): 9.131000 64.27900 x,y,z range (A): 54.58400 58.35500 55.14800 scale (grids/A): 1.830177 object centre (A): 18.76600 3.872499 36.70500 number of atom coordinates read : 2461 total number of charged atoms : 2316 net assigned charge : -1.999992 assigned positive charge : 362.6572 centred at (gu) : 88.28012 92.43596 87.52875 assigned negative charge : -364.6577 centred at (gu) : 87.82102 92.06087 87.50705 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 65655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 21533 mr = 43990 m= 2868 mr = 15088 m= 117 mr = 1460 m= 0 mr = 23 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18159 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) : 0.6100591 object centre at (A) : 18.76600 3.872499 36.70500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9845806E-02 -7.2879520E-05 midg,1,midg; midg,igrid,midg -7.1352483E-03 1.6210988E-02 1,midg,midg; igrid,midg,midg -7.2006830E-03 1.2158282E-02 gauss-seidel spectral radius is 0.9985024 estimated iterations to convergence 205 setup time was (sec) 0.8400000 now iterating at: 14:41:52 rms-change max change #iterations 3.755477 161.3613 at 10iterations 1.680858 58.57623 at 20iterations 0.7606966 28.71998 at 30iterations 0.3418522 12.16555 at 40iterations 0.1544933 5.174679 at 50iterations 6.9614939E-02 2.349945 at 60iterations 3.1548187E-02 1.052918 at 70iterations 1.4202862E-02 0.4776020 at 80iterations 6.4167641E-03 0.2691116 at 90iterations 2.9000402E-03 9.7884178E-02 at 100iterations 1.3094837E-03 4.5733452E-02 at 110iterations 5.9320877E-04 2.0204544E-02 at 120iterations finished qdiffx linear iterations at : 14:42:02 total time elapsed so far: 10.34000 # loops : 120 mean,max change (kT/e) : 5.9320877E-04 2.0204544E-02 energy calculations done at 10.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.51000 DelPhi exited at 14:42:03 10.518u 0.464s 0:11.39 96.3% 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 Oct 10 2011 at 14:42:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 2.745266 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): -8.526000 46.05800 ymin,ymax (A): -25.30500 33.05000 zmin,zma (A): 9.131000 64.27900 x,y,z range (A): 54.58400 58.35500 55.14800 scale (grids/A): 2.745266 object centre (A): 18.76600 3.872499 36.70500 number of atom coordinates read : 2461 total number of charged atoms : 2316 net assigned charge : -1.999992 assigned positive charge : 362.6572 centred at (gu) : 87.42010 93.65387 86.29308 assigned negative charge : -364.6577 centred at (gu) : 86.73146 93.09127 86.26064 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 152378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 71721 mr = 107609 m= 23151 mr = 57001 m= 4712 mr = 17597 m= 553 mr = 3213 m= 26 mr = 283 m= 0 mr = 4 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 66834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 18525 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) : 1.830177 object centre at (A) : 18.76600 3.872499 36.70500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7198083 0.1306041 midg,1,midg; midg,igrid,midg -6.1294679E-02 0.2069997 1,midg,midg; igrid,midg,midg -4.7044005E-02 0.1123091 gauss-seidel spectral radius is 0.9992195 estimated iterations to convergence 283 setup time was (sec) 1.800000 now iterating at: 14:42:05 rms-change max change #iterations 9.043144 400.2593 at 10iterations 5.212030 111.8645 at 20iterations 2.976203 60.44179 at 30iterations 1.700733 41.12025 at 40iterations 0.9648406 18.52634 at 50iterations 0.5496923 11.36437 at 60iterations 0.3108955 6.873849 at 70iterations 0.1766743 3.696338 at 80iterations 9.9971063E-02 1.918811 at 90iterations 5.6575086E-02 1.044072 at 100iterations 3.1974744E-02 0.6565676 at 110iterations 1.8106421E-02 0.3860183 at 120iterations 1.0235822E-02 0.2011395 at 130iterations 5.7859230E-03 0.1218371 at 140iterations 3.2682228E-03 6.3169241E-02 at 150iterations 1.8504802E-03 3.5444260E-02 at 160iterations 1.0451939E-03 2.1892548E-02 at 170iterations 5.8992550E-04 1.1833191E-02 at 180iterations finished qdiffx linear iterations at : 14:42:21 total time elapsed so far: 17.70000 # loops : 180 mean,max change (kT/e) : 5.8992550E-04 1.1833191E-02 energy calculations done at 17.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.86000 DelPhi exited at 14:42:22 17.869u 0.495s 0:18.91 97.0% 0+0k 0+0io 0pf+0w