Sat Oct 8 16:00:35 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 Sat Oct 8 2011 at 16:00:35 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 = 2286 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: 0.6611694 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): -2.217000 45.63000 ymin,ymax (A): -15.68200 29.40700 zmin,zma (A): -16.92300 36.92100 x,y,z range (A): 47.84700 45.08900 53.84400 scale (grids/A): 0.6611694 object centre (A): 21.70650 6.862500 9.998999 number of atom coordinates read : 2286 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 90.74031 88.56204 90.09792 assigned negative charge : -338.3788 centred at (gu) : 90.79374 88.69177 90.14091 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6798 nv = 96 ne = 84 npr = 45185 no. pairs analyzed = 45185 no. exposed pairs = 3012 no. arc points = 20573 no. surface atoms = 1025 nbur = 1261 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3707 m= 0 mr = 73 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2900000 number of dielectric boundary points 3442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2007 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8157 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7440334E-08 2.5864517E-09 midg,1,midg; midg,igrid,midg 4.4504983E-08 -9.5666390E-09 1,midg,midg; igrid,midg,midg 1.6866359E-08 6.7996581E-10 gauss-seidel spectral radius is 0.9881191 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 16:00:36 rms-change max change #iterations 0.1528436 21.99891 at 10iterations 1.6317356E-02 2.504345 at 20iterations 1.8014467E-03 0.2469431 at 30iterations 2.2820802E-04 3.2358170E-02 at 40iterations 4.4994867E-05 7.2402954E-03 at 50iterations finished qdiffx linear iterations at : 16:00:40 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 4.4994867E-05 7.2402954E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 16:00:40 4.485u 0.346s 0:05.11 94.3% 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 Sat Oct 8 2011 at 16:00:40 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2286 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: 1.983508 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): -2.217000 45.63000 ymin,ymax (A): -15.68200 29.40700 zmin,zma (A): -16.92300 36.92100 x,y,z range (A): 47.84700 45.08900 53.84400 scale (grids/A): 1.983508 object centre (A): 21.70650 6.862500 9.998999 number of atom coordinates read : 2286 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 92.22050 85.68555 90.29363 assigned negative charge : -338.3788 centred at (gu) : 92.38110 86.07525 90.42268 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20573 grid for indexing accessible points = 1.400000 m= 27075 mr = 50816 m= 4929 mr = 19882 m= 388 mr = 3390 m= 4 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 325 time to turn everything in is 0.6000000 number of dielectric boundary points 31631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17623 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) : 0.6611694 object centre at (A) : 21.70650 6.862500 9.998999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8104991E-02 -2.0740036E-02 midg,1,midg; midg,igrid,midg 3.3334497E-02 -4.7710147E-03 1,midg,midg; igrid,midg,midg 8.5690739E-03 -4.1741766E-02 gauss-seidel spectral radius is 0.9987112 estimated iterations to convergence 221 setup time was (sec) 0.9100000 now iterating at: 16:00:42 rms-change max change #iterations 4.281595 191.6727 at 10iterations 2.043447 67.06220 at 20iterations 0.9775733 31.66485 at 30iterations 0.4690399 15.35669 at 40iterations 0.2250281 7.164601 at 50iterations 0.1076559 3.498314 at 60iterations 5.1844060E-02 1.602032 at 70iterations 2.4761381E-02 0.7737103 at 80iterations 1.1858675E-02 0.3691065 at 90iterations 5.6859301E-03 0.1832666 at 100iterations 2.7291884E-03 8.3986282E-02 at 110iterations 1.3166637E-03 4.2870522E-02 at 120iterations finished qdiffx linear iterations at : 16:00:52 total time elapsed so far: 11.00000 # loops : 120 mean,max change (kT/e) : 1.3166637E-03 4.2870522E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.16000 DelPhi exited at 16:00:52 11.167u 0.438s 0:11.87 97.6% 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 16:00:52 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 = 2286 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: 2.975262 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): -2.217000 45.63000 ymin,ymax (A): -15.68200 29.40700 zmin,zma (A): -16.92300 36.92100 x,y,z range (A): 47.84700 45.08900 53.84400 scale (grids/A): 2.975262 object centre (A): 21.70650 6.862500 9.998999 number of atom coordinates read : 2286 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 93.33069 83.52829 90.44028 assigned negative charge : -338.3788 centred at (gu) : 93.57161 84.11287 90.63396 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 169888 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20573 grid for indexing accessible points = 1.400000 m= 86058 mr = 123151 m= 33155 mr = 70132 m= 9208 mr = 26852 m= 1729 mr = 7265 m= 115 mr = 1294 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1194 time to turn everything in is 1.600000 number of dielectric boundary points 71393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 17840 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) : 1.983508 object centre at (A) : 21.70650 6.862500 9.998999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1878868 -0.2613916 midg,1,midg; midg,igrid,midg 0.2650014 -6.5003119E-02 1,midg,midg; igrid,midg,midg 7.4873418E-02 -0.6407098 gauss-seidel spectral radius is 0.9992808 estimated iterations to convergence 294 setup time was (sec) 1.930000 now iterating at: 16:00:54 rms-change max change #iterations 9.846107 473.6122 at 10iterations 5.792328 134.2957 at 20iterations 3.401007 72.79947 at 30iterations 1.992757 37.95736 at 40iterations 1.164433 27.11185 at 50iterations 0.6803733 14.97982 at 60iterations 0.3969760 7.420624 at 70iterations 0.2309020 4.498899 at 80iterations 0.1341030 2.499163 at 90iterations 7.8023568E-02 1.572517 at 100iterations 4.5246501E-02 0.8611400 at 110iterations 2.6319414E-02 0.4721527 at 120iterations 1.5256649E-02 0.2772989 at 130iterations 8.8403523E-03 0.1617813 at 140iterations 5.1470050E-03 9.4814301E-02 at 150iterations 2.9908663E-03 5.3001404E-02 at 160iterations 1.7379632E-03 3.2207966E-02 at 170iterations 1.0158469E-03 1.8472433E-02 at 180iterations finished qdiffx linear iterations at : 16:01:10 total time elapsed so far: 17.82000 # loops : 180 mean,max change (kT/e) : 1.0158469E-03 1.8472433E-02 energy calculations done at 17.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.98000 DelPhi exited at 16:01:11 17.983u 0.458s 0:18.69 98.6% 0+0k 0+0io 0pf+0w