Mon Oct 10 00:06:15 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 Mon Oct 10 2011 at 00:06:16 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3098 !!! WARNING: SEP 140 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: 0.6197556 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): -34.65600 19.53100 ymin,ymax (A): -13.56600 37.68000 zmin,zma (A): -14.78100 42.66100 x,y,z range (A): 54.18700 51.24600 57.44200 scale (grids/A): 0.6197556 object centre (A): -7.562501 12.05700 13.94000 number of atom coordinates read : 3098 total number of charged atoms : 2953 net assigned charge : 1.025010 assigned positive charge : 468.6940 centred at (gu) : 90.93032 90.44942 91.28043 assigned negative charge : -467.6702 centred at (gu) : 90.89188 90.35634 91.18974 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7907 nv = 96 ne = 84 npr = 61573 no. pairs analyzed = 61573 no. exposed pairs = 4054 no. arc points = 28864 no. surface atoms = 1350 nbur = 1748 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4129 m= 0 mr = 40 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2300000 number of dielectric boundary points 4135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2823 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9661999E-09 1.0374230E-08 midg,1,midg; midg,igrid,midg -6.1567569E-09 8.8051255E-09 1,midg,midg; igrid,midg,midg -1.9528210E-09 4.5412731E-09 gauss-seidel spectral radius is 0.9865659 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 00:06:16 rms-change max change #iterations 0.1365362 21.15566 at 10iterations 1.2456214E-02 1.774580 at 20iterations 1.1481337E-03 0.1686449 at 30iterations 1.0673851E-04 1.5176415E-02 at 40iterations 9.7480079E-06 1.3711452E-03 at 50iterations finished qdiffx linear iterations at : 00:06:19 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 9.7480079E-06 1.3711452E-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) 3.420000 DelPhi exited at 00:06:19 3.427u 0.182s 0:03.87 93.0% 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 Mon Oct 10 2011 at 00:06:19 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3098 !!! WARNING: SEP 140 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.859267 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): -34.65600 19.53100 ymin,ymax (A): -13.56600 37.68000 zmin,zma (A): -14.78100 42.66100 x,y,z range (A): 54.18700 51.24600 57.44200 scale (grids/A): 1.859267 object centre (A): -7.562501 12.05700 13.94000 number of atom coordinates read : 3098 total number of charged atoms : 2953 net assigned charge : 1.025010 assigned positive charge : 468.6940 centred at (gu) : 92.79013 91.34737 93.84060 assigned negative charge : -467.6702 centred at (gu) : 92.67542 91.06871 93.56879 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28864 grid for indexing accessible points = 1.400000 m= 28483 mr = 58689 m= 3749 mr = 19977 m= 184 mr = 2034 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 0.4200000 number of dielectric boundary points 38197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 23130 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) : 0.6197556 object centre at (A) : -7.562501 12.05700 13.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7379327E-03 9.7189154E-03 midg,1,midg; midg,igrid,midg -8.5010957E-03 1.1019526E-02 1,midg,midg; igrid,midg,midg -1.8752446E-02 2.6693996E-03 gauss-seidel spectral radius is 0.9986305 estimated iterations to convergence 214 setup time was (sec) 0.6400000 now iterating at: 00:06:20 rms-change max change #iterations 4.509372 179.8095 at 10iterations 2.096695 65.07561 at 20iterations 0.9767104 31.05721 at 30iterations 0.4567684 13.87302 at 40iterations 0.2148110 7.256497 at 50iterations 9.9621922E-02 3.176392 at 60iterations 4.6829674E-02 1.520962 at 70iterations 2.1879787E-02 0.6889067 at 80iterations 1.0186221E-02 0.3322563 at 90iterations 4.7701644E-03 0.1568749 at 100iterations 2.2356387E-03 6.9271088E-02 at 110iterations 1.0411370E-03 2.8955460E-02 at 120iterations finished qdiffx linear iterations at : 00:06:27 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 1.0411370E-03 2.8955460E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 00:06:28 7.926u 0.212s 0:08.51 95.5% 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 00:06:28 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3098 !!! WARNING: SEP 140 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.788900 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): -34.65600 19.53100 ymin,ymax (A): -13.56600 37.68000 zmin,zma (A): -14.78100 42.66100 x,y,z range (A): 54.18700 51.24600 57.44200 scale (grids/A): 2.788900 object centre (A): -7.562501 12.05700 13.94000 number of atom coordinates read : 3098 total number of charged atoms : 2953 net assigned charge : 1.025010 assigned positive charge : 468.6940 centred at (gu) : 94.18497 92.02094 95.76059 assigned negative charge : -467.6702 centred at (gu) : 94.01302 91.60310 95.35294 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 200485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28864 grid for indexing accessible points = 1.400000 m= 94855 mr = 142918 m= 30740 mr = 75857 m= 6368 mr = 23568 m= 733 mr = 4333 m= 34 mr = 411 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 5357 time to turn everything in is 1.060000 number of dielectric boundary points 86126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 23622 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) : 1.859267 object centre at (A) : -7.562501 12.05700 13.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1005722 -4.5414292E-03 midg,1,midg; midg,igrid,midg -1.1534394E-02 -9.0113759E-02 1,midg,midg; igrid,midg,midg -0.2953153 -4.2624284E-02 gauss-seidel spectral radius is 0.9992791 estimated iterations to convergence 294 setup time was (sec) 1.300000 now iterating at: 00:06:29 rms-change max change #iterations 10.83044 329.9633 at 10iterations 6.488665 137.4319 at 20iterations 3.851931 88.13107 at 30iterations 2.268945 44.54158 at 40iterations 1.334740 35.27621 at 50iterations 0.7804027 14.49924 at 60iterations 0.4557378 8.861394 at 70iterations 0.2655268 5.209610 at 80iterations 0.1542332 2.865540 at 90iterations 8.9738503E-02 1.502963 at 100iterations 5.2118823E-02 0.9291086 at 110iterations 3.0217409E-02 0.5442772 at 120iterations 1.7555224E-02 0.3239566 at 130iterations 1.0158200E-02 0.1909409 at 140iterations 5.8881990E-03 0.1102033 at 150iterations 3.4051370E-03 5.8261871E-02 at 160iterations 1.9740609E-03 3.9215088E-02 at 170iterations 1.1439871E-03 2.0671844E-02 at 180iterations finished qdiffx linear iterations at : 00:06:41 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.1439871E-03 2.0671844E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 00:06:41 13.011u 0.212s 0:13.48 98.0% 0+0k 0+0io 0pf+0w