Tue Oct 11 06:17:01 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 06:17:01 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.6845627 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): 15.67100 62.80700 ymin,ymax (A): -3.493000 33.73000 zmin,zma (A): 19.96800 71.97200 x,y,z range (A): 47.13600 37.22300 52.00400 scale (grids/A): 0.6845627 object centre (A): 39.23900 15.11850 45.97000 number of atom coordinates read : 2125 total number of charged atoms : 1993 net assigned charge : 6.420009 assigned positive charge : 326.0059 centred at (gu) : 91.41669 89.60411 89.04122 assigned negative charge : -319.5861 centred at (gu) : 91.54303 89.63432 88.96021 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6692 nv = 96 ne = 84 npr = 42449 no. pairs analyzed = 42449 no. exposed pairs = 2600 no. arc points = 17748 no. surface atoms = 888 nbur = 1237 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3796 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6215248E-09 4.6065662E-08 midg,1,midg; midg,igrid,midg 4.4032056E-08 2.1094108E-08 1,midg,midg; igrid,midg,midg 5.2015793E-08 -9.2585237E-09 gauss-seidel spectral radius is 0.9888868 estimated iterations to convergence 77 setup time was (sec) 0.5800000 now iterating at: 06:17:02 rms-change max change #iterations 0.1774507 28.35361 at 10iterations 2.0595439E-02 2.809669 at 20iterations 2.5532402E-03 0.3947220 at 30iterations 4.2035920E-04 5.9120178E-02 at 40iterations 1.1328042E-04 1.7929077E-02 at 50iterations finished qdiffx linear iterations at : 06:17:07 total time elapsed so far: 4.740000 # loops : 50 mean,max change (kT/e) : 1.1328042E-04 1.7929077E-02 energy calculations done at 4.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.920000 DelPhi exited at 06:17:07 4.923u 0.413s 0:05.66 94.1% 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 Tue Oct 11 2011 at 06:17:07 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.053688 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): 15.67100 62.80700 ymin,ymax (A): -3.493000 33.73000 zmin,zma (A): 19.96800 71.97200 x,y,z range (A): 47.13600 37.22300 52.00400 scale (grids/A): 2.053688 object centre (A): 39.23900 15.11850 45.97000 number of atom coordinates read : 2125 total number of charged atoms : 1993 net assigned charge : 6.420009 assigned positive charge : 326.0059 centred at (gu) : 94.24965 88.81232 87.12331 assigned negative charge : -319.5861 centred at (gu) : 94.62934 88.90298 86.88079 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17748 grid for indexing accessible points = 1.400000 m= 27795 mr = 50256 m= 4955 mr = 20943 m= 417 mr = 3226 m= 5 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 29882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15798 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) : 0.6845627 object centre at (A) : 39.23900 15.11850 45.97000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7438996E-02 4.6108373E-02 midg,1,midg; midg,igrid,midg 2.3373703E-02 8.0531659E-03 1,midg,midg; igrid,midg,midg 2.5962437E-02 1.4692228E-02 gauss-seidel spectral radius is 0.9987636 estimated iterations to convergence 225 setup time was (sec) 0.9900000 now iterating at: 06:17:09 rms-change max change #iterations 4.406011 182.9004 at 10iterations 2.141613 74.14322 at 20iterations 1.038900 35.63720 at 30iterations 0.5082251 16.56658 at 40iterations 0.2472985 7.589269 at 50iterations 0.1198961 4.222377 at 60iterations 5.8394473E-02 2.196686 at 70iterations 2.8466724E-02 0.9125214 at 80iterations 1.3967020E-02 0.4453921 at 90iterations 6.8361573E-03 0.2107199 at 100iterations 3.3628037E-03 9.8995209E-02 at 110iterations 1.6976265E-03 6.4684629E-02 at 120iterations finished qdiffx linear iterations at : 06:17:19 total time elapsed so far: 11.63000 # loops : 120 mean,max change (kT/e) : 1.6976265E-03 6.4684629E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 06:17:20 11.802u 0.489s 0:12.73 96.4% 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 06:17:20 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.080532 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): 15.67100 62.80700 ymin,ymax (A): -3.493000 33.73000 zmin,zma (A): 19.96800 71.97200 x,y,z range (A): 47.13600 37.22300 52.00400 scale (grids/A): 3.080532 object centre (A): 39.23900 15.11850 45.97000 number of atom coordinates read : 2125 total number of charged atoms : 1993 net assigned charge : 6.420009 assigned positive charge : 326.0059 centred at (gu) : 96.37460 88.21840 85.68498 assigned negative charge : -319.5861 centred at (gu) : 96.94380 88.35447 85.32112 start vw surface at 0.1000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 164445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17748 grid for indexing accessible points = 1.400000 m= 88126 mr = 121292 m= 34125 mr = 73041 m= 9207 mr = 27816 m= 1673 mr = 6980 m= 170 mr = 1227 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 67299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15944 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) : 2.053688 object centre at (A) : 39.23900 15.11850 45.97000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2840405 0.3661843 midg,1,midg; midg,igrid,midg 0.2183315 5.4581475E-02 1,midg,midg; igrid,midg,midg 0.2286360 0.3900373 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 2.230000 now iterating at: 06:17:23 rms-change max change #iterations 10.01078 424.5401 at 10iterations 5.862404 122.6343 at 20iterations 3.450809 78.09978 at 30iterations 2.022539 42.50086 at 40iterations 1.182373 24.76440 at 50iterations 0.6909056 14.07281 at 60iterations 0.4032148 7.725216 at 70iterations 0.2348651 4.518311 at 80iterations 0.1369289 2.538673 at 90iterations 7.9606406E-02 1.535952 at 100iterations 4.6477657E-02 0.8806324 at 110iterations 2.7206840E-02 0.5799503 at 120iterations 1.6000073E-02 0.3038616 at 130iterations 9.4931368E-03 0.1952648 at 140iterations 5.7509653E-03 0.1069183 at 150iterations 3.5811786E-03 6.7993164E-02 at 160iterations 2.3400371E-03 4.2980194E-02 at 170iterations 1.6185218E-03 3.0996323E-02 at 180iterations finished qdiffx linear iterations at : 06:17:40 total time elapsed so far: 19.90000 # loops : 180 mean,max change (kT/e) : 1.6185218E-03 3.0996323E-02 energy calculations done at 19.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.06000 DelPhi exited at 06:17:41 20.062u 0.547s 0:20.92 98.4% 0+0k 0+0io 0pf+0w