Sat Oct 8 18:26:33 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 Sat Oct 8 2011 at 18:26:33 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3420 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: 0.5807220 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): -26.41300 27.01000 ymin,ymax (A): -34.10200 27.20100 zmin,zma (A): -39.99700 18.24200 x,y,z range (A): 53.42300 61.30300 58.23900 scale (grids/A): 0.5807220 object centre (A): 0.2985001 -3.450499 -10.87750 number of atom coordinates read : 3420 total number of charged atoms : 3274 net assigned charge : 7.500026 assigned positive charge : 522.4993 centred at (gu) : 89.05391 89.08832 88.80964 assigned negative charge : -515.0007 centred at (gu) : 89.09322 89.12604 88.84603 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7894 nv = 96 ne = 84 npr = 65588 no. pairs analyzed = 65588 no. exposed pairs = 4721 no. arc points = 34057 no. surface atoms = 1549 nbur = 1871 mkacc time = 0.1900000 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= 414 mr = 3964 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.4300000 number of dielectric boundary points 4311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3499 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4087642E-09 5.3818133E-10 midg,1,midg; midg,igrid,midg 3.2366565E-09 5.4213822E-10 1,midg,midg; igrid,midg,midg 3.3143555E-09 5.0477744E-10 gauss-seidel spectral radius is 0.9847461 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 18:26:34 rms-change max change #iterations 0.1083890 15.88504 at 10iterations 9.5345983E-03 1.395710 at 20iterations 1.4658424E-03 0.2228317 at 30iterations 3.9054168E-04 6.1222076E-02 at 40iterations 1.1688275E-04 1.8234253E-02 at 50iterations finished qdiffx linear iterations at : 18:26:37 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.1688275E-04 1.8234253E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 18:26:38 4.256u 0.280s 0:04.81 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 Sat Oct 8 2011 at 18:26:38 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3420 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: 1.742166 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): -26.41300 27.01000 ymin,ymax (A): -34.10200 27.20100 zmin,zma (A): -39.99700 18.24200 x,y,z range (A): 53.42300 61.30300 58.23900 scale (grids/A): 1.742166 object centre (A): 0.2985001 -3.450499 -10.87750 number of atom coordinates read : 3420 total number of charged atoms : 3274 net assigned charge : 7.500026 assigned positive charge : 522.4993 centred at (gu) : 87.16091 87.26403 86.42815 assigned negative charge : -515.0007 centred at (gu) : 87.27928 87.37743 86.53755 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34057 grid for indexing accessible points = 1.400000 m= 29838 mr = 56159 m= 4403 mr = 20770 m= 169 mr = 2483 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2795 time to turn everything in is 0.7600000 number of dielectric boundary points 40189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 25396 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) : 0.5807220 object centre at (A) : 0.2985001 -3.450499 -10.87750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0980116E-02 7.5977421E-03 midg,1,midg; midg,igrid,midg 1.4216564E-02 1.5498463E-02 1,midg,midg; igrid,midg,midg 4.8483866E-03 -1.0443163E-03 gauss-seidel spectral radius is 0.9984778 estimated iterations to convergence 203 setup time was (sec) 1.070000 now iterating at: 18:26:39 rms-change max change #iterations 4.229172 184.7563 at 10iterations 1.890712 73.06996 at 20iterations 0.8489069 29.41117 at 30iterations 0.3818931 12.13470 at 40iterations 0.1715899 5.694394 at 50iterations 7.7061377E-02 2.418438 at 60iterations 3.4798052E-02 1.176506 at 70iterations 1.5660919E-02 0.5166264 at 80iterations 7.1743960E-03 0.2407605 at 90iterations 3.2953057E-03 0.1077638 at 100iterations 1.5616608E-03 5.7945251E-02 at 110iterations 7.6704135E-04 2.6081085E-02 at 120iterations finished qdiffx linear iterations at : 18:26:48 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 7.6704135E-04 2.6081085E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 18:26:48 9.961u 0.328s 0:10.56 97.3% 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 18:26:48 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3420 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: 2.613249 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): -26.41300 27.01000 ymin,ymax (A): -34.10200 27.20100 zmin,zma (A): -39.99700 18.24200 x,y,z range (A): 53.42300 61.30300 58.23900 scale (grids/A): 2.613249 object centre (A): 0.2985001 -3.450499 -10.87750 number of atom coordinates read : 3420 total number of charged atoms : 3274 net assigned charge : 7.500026 assigned positive charge : 522.4993 centred at (gu) : 85.74097 85.89588 84.64185 assigned negative charge : -515.0007 centred at (gu) : 85.91882 86.06599 84.80633 start vw surface at 0.1900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 196636 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34057 grid for indexing accessible points = 1.400000 m= 97093 mr = 137060 m= 34064 mr = 76651 m= 7638 mr = 26202 m= 875 mr = 5489 m= 18 mr = 414 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 9570 time to turn everything in is 1.950000 number of dielectric boundary points 90508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 26183 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) : 1.742166 object centre at (A) : 0.2985001 -3.450499 -10.87750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2345926 0.1329572 midg,1,midg; midg,igrid,midg -9.2227049E-02 0.2545370 1,midg,midg; igrid,midg,midg 1.0161418E-02 3.4262255E-02 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 2.300000 now iterating at: 18:26:51 rms-change max change #iterations 10.59727 343.6196 at 10iterations 6.256441 153.4607 at 20iterations 3.671255 91.01334 at 30iterations 2.138644 49.11581 at 40iterations 1.239264 25.45083 at 50iterations 0.7160481 14.68210 at 60iterations 0.4114361 7.996302 at 70iterations 0.2370508 4.452897 at 80iterations 0.1364560 2.814375 at 90iterations 7.8256294E-02 1.404476 at 100iterations 4.4840001E-02 0.8332539 at 110iterations 2.5737414E-02 0.4680119 at 120iterations 1.4776436E-02 0.3119621 at 130iterations 8.4758149E-03 0.1645050 at 140iterations 4.8640892E-03 8.7486267E-02 at 150iterations 2.8046770E-03 5.3053379E-02 at 160iterations 1.6319402E-03 3.1929016E-02 at 170iterations 9.5724035E-04 1.7703056E-02 at 180iterations finished qdiffx linear iterations at : 18:27:06 total time elapsed so far: 17.27000 # loops : 180 mean,max change (kT/e) : 9.5724035E-04 1.7703056E-02 energy calculations done at 17.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.45000 DelPhi exited at 18:27:06 17.454u 0.351s 0:18.08 98.4% 0+0k 0+0io 0pf+0w