Tue Oct 11 08:10:24 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 08:10:24 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: WAT 2 has a net charge of -0.8340 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: 0.5775002 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): -22.03700 28.46600 ymin,ymax (A): 21.88400 83.52900 zmin,zma (A): 2.340000 51.99300 x,y,z range (A): 50.50300 61.64500 49.65300 scale (grids/A): 0.5775002 object centre (A): 3.214500 52.70650 27.16650 number of atom coordinates read : 2325 total number of charged atoms : 2185 net assigned charge : 3.666011 assigned positive charge : 349.4163 centred at (gu) : 90.01619 86.83549 91.94511 assigned negative charge : -345.7509 centred at (gu) : 89.86147 86.78750 91.83319 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5206 nv = 96 ne = 84 npr = 46368 no. pairs analyzed = 46368 no. exposed pairs = 3088 no. arc points = 22042 no. surface atoms = 1027 nbur = 1298 mkacc time = 9.9999994E-02 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 = 1.484000 m= 226 mr = 2617 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2600000 number of dielectric boundary points 2802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2240 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6510 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4796901E-10 3.8530414E-09 midg,1,midg; midg,igrid,midg -1.3388593E-10 7.0358014E-10 1,midg,midg; igrid,midg,midg -1.7206763E-09 3.0768952E-09 gauss-seidel spectral radius is 0.9844760 estimated iterations to convergence 66 setup time was (sec) 0.4700000 now iterating at: 08:10:24 rms-change max change #iterations 8.5634641E-02 15.47861 at 10iterations 6.6387723E-03 1.143690 at 20iterations 6.3171197E-04 0.1157513 at 30iterations 1.1682042E-04 3.1362534E-02 at 40iterations 3.2686359E-05 9.2391968E-03 at 50iterations finished qdiffx linear iterations at : 08:10:27 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.2686359E-05 9.2391968E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:10:27 3.131u 0.166s 0:03.63 90.6% 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 Tue Oct 11 2011 at 08:10:27 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: WAT 2 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.732501 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): -22.03700 28.46600 ymin,ymax (A): 21.88400 83.52900 zmin,zma (A): 2.340000 51.99300 x,y,z range (A): 50.50300 61.64500 49.65300 scale (grids/A): 1.732501 object centre (A): 3.214500 52.70650 27.16650 number of atom coordinates read : 2325 total number of charged atoms : 2185 net assigned charge : 3.666011 assigned positive charge : 349.4163 centred at (gu) : 90.04822 80.50603 95.83500 assigned negative charge : -345.7509 centred at (gu) : 89.58440 80.36243 95.49939 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 56728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22042 grid for indexing accessible points = 1.400000 m= 17582 mr = 37418 m= 2049 mr = 11942 m= 73 mr = 1051 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 351 time to turn everything in is 0.4300000 number of dielectric boundary points 26001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 16892 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) : 0.5775002 object centre at (A) : 3.214500 52.70650 27.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6781670E-03 1.3573903E-02 midg,1,midg; midg,igrid,midg 2.4757110E-02 2.5301572E-02 1,midg,midg; igrid,midg,midg -8.4249247E-03 1.4600548E-02 gauss-seidel spectral radius is 0.9983189 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 08:10:28 rms-change max change #iterations 3.304764 173.0060 at 10iterations 1.414037 64.57628 at 20iterations 0.6065129 22.81495 at 30iterations 0.2613804 9.417068 at 40iterations 0.1122382 4.363388 at 50iterations 4.8388794E-02 1.770527 at 60iterations 2.0871967E-02 0.8140860 at 70iterations 9.0097068E-03 0.3632660 at 80iterations 3.8980141E-03 0.1490631 at 90iterations 1.7263121E-03 7.7125549E-02 at 100iterations 7.8749558E-04 3.1845093E-02 at 110iterations 3.8512950E-04 1.8350363E-02 at 120iterations finished qdiffx linear iterations at : 08:10:35 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 3.8512950E-04 1.8350363E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 08:10:35 7.248u 0.180s 0:08.04 92.2% 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 08:10:35 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: WAT 2 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.598751 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): -22.03700 28.46600 ymin,ymax (A): 21.88400 83.52900 zmin,zma (A): 2.340000 51.99300 x,y,z range (A): 50.50300 61.64500 49.65300 scale (grids/A): 2.598751 object centre (A): 3.214500 52.70650 27.16650 number of atom coordinates read : 2325 total number of charged atoms : 2185 net assigned charge : 3.666011 assigned positive charge : 349.4163 centred at (gu) : 90.07225 75.75903 98.75253 assigned negative charge : -345.7509 centred at (gu) : 89.37653 75.54361 98.24914 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 131556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22042 grid for indexing accessible points = 1.400000 m= 60364 mr = 91713 m= 17821 mr = 47433 m= 3272 mr = 13202 m= 299 mr = 2189 m= 14 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1237 time to turn everything in is 1.030000 number of dielectric boundary points 58607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 17471 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) : 1.732501 object centre at (A) : 3.214500 52.70650 27.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2303046E-02 0.1346273 midg,1,midg; midg,igrid,midg 0.3281312 0.3629017 1,midg,midg; igrid,midg,midg -7.9376787E-02 0.1991637 gauss-seidel spectral radius is 0.9991652 estimated iterations to convergence 273 setup time was (sec) 1.340000 now iterating at: 08:10:37 rms-change max change #iterations 8.370945 273.6563 at 10iterations 4.754938 130.1084 at 20iterations 2.690825 68.67875 at 30iterations 1.513164 38.54284 at 40iterations 0.8484659 22.21994 at 50iterations 0.4744145 11.56965 at 60iterations 0.2654093 5.973476 at 70iterations 0.1476362 3.316305 at 80iterations 8.2157001E-02 1.784043 at 90iterations 4.5752566E-02 1.031715 at 100iterations 2.5431320E-02 0.6752539 at 110iterations 1.4149257E-02 0.3547897 at 120iterations 7.8976024E-03 0.1719794 at 130iterations 4.4174949E-03 0.1040218 at 140iterations 2.4805476E-03 5.6653976E-02 at 150iterations 1.4182813E-03 4.0872574E-02 at 160iterations 8.2853914E-04 2.2426605E-02 at 170iterations 5.0756679E-04 1.4879227E-02 at 180iterations finished qdiffx linear iterations at : 08:10:47 total time elapsed so far: 11.69000 # loops : 180 mean,max change (kT/e) : 5.0756679E-04 1.4879227E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 08:10:48 11.873u 0.209s 0:12.53 96.3% 0+0k 0+0io 0pf+0w