Sat Oct 15 11:52:51 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 15 2011 at 11:52:51 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2244 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6573602 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): -29.85800 22.25400 ymin,ymax (A): 27.50000 71.23700 zmin,zma (A): -13.20200 40.95400 x,y,z range (A): 52.11200 43.73700 54.15600 scale (grids/A): 0.6573602 object centre (A): -3.802000 49.36850 13.87600 number of atom coordinates read : 2244 total number of charged atoms : 2110 net assigned charge : 12.51402 assigned positive charge : 328.5036 centred at (gu) : 91.47606 91.45295 89.43042 assigned negative charge : -315.9903 centred at (gu) : 91.42752 91.38326 89.41903 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 44836 no. pairs analyzed = 44836 no. exposed pairs = 3031 no. arc points = 21571 no. surface atoms = 1018 nbur = 1226 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3489 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2080 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0823770E-08 2.7556531E-08 midg,1,midg; midg,igrid,midg 1.4110712E-08 5.3377576E-08 1,midg,midg; igrid,midg,midg 1.6398356E-08 4.9334862E-08 gauss-seidel spectral radius is 0.9879850 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 11:52:51 rms-change max change #iterations 0.1492602 25.01815 at 10iterations 1.5626071E-02 2.528419 at 20iterations 1.7137395E-03 0.2348938 at 30iterations 2.1492866E-04 3.6178589E-02 at 40iterations 3.4481309E-05 6.1912537E-03 at 50iterations finished qdiffx linear iterations at : 11:52:54 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.4481309E-05 6.1912537E-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 11:52:55 3.419u 0.187s 0:03.94 91.1% 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 15 2011 at 11:52:55 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2244 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.972081 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): -29.85800 22.25400 ymin,ymax (A): 27.50000 71.23700 zmin,zma (A): -13.20200 40.95400 x,y,z range (A): 52.11200 43.73700 54.15600 scale (grids/A): 1.972081 object centre (A): -3.802000 49.36850 13.87600 number of atom coordinates read : 2244 total number of charged atoms : 2110 net assigned charge : 12.51402 assigned positive charge : 328.5036 centred at (gu) : 94.42780 94.35869 88.29103 assigned negative charge : -315.9903 centred at (gu) : 94.28268 94.14983 88.25712 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21571 grid for indexing accessible points = 1.400000 m= 26946 mr = 47575 m= 4975 mr = 19396 m= 409 mr = 3089 m= 8 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.3600000 number of dielectric boundary points 33673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 16648 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) : 0.6573602 object centre at (A) : -3.802000 49.36850 13.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7411704E-02 4.9243756E-02 midg,1,midg; midg,igrid,midg 3.6686102E-03 3.6524974E-02 1,midg,midg; igrid,midg,midg 5.4942708E-02 3.6191575E-02 gauss-seidel spectral radius is 0.9986988 estimated iterations to convergence 220 setup time was (sec) 0.5800000 now iterating at: 11:52:56 rms-change max change #iterations 4.043255 195.0133 at 10iterations 1.923563 80.34804 at 20iterations 0.9137930 33.06223 at 30iterations 0.4348712 13.80418 at 40iterations 0.2069780 7.576241 at 50iterations 9.8700732E-02 3.102644 at 60iterations 4.6890669E-02 1.603535 at 70iterations 2.2388117E-02 0.7412803 at 80iterations 1.0686424E-02 0.3625698 at 90iterations 5.1133074E-03 0.1646795 at 100iterations 2.4434789E-03 7.3431969E-02 at 110iterations 1.1762013E-03 4.2015076E-02 at 120iterations finished qdiffx linear iterations at : 11:53:03 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.1762013E-03 4.2015076E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 11:53:03 7.888u 0.200s 0:08.34 96.8% 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 15 2011 at 11:53:03 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2244 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.958121 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): -29.85800 22.25400 ymin,ymax (A): 27.50000 71.23700 zmin,zma (A): -13.20200 40.95400 x,y,z range (A): 52.11200 43.73700 54.15600 scale (grids/A): 2.958121 object centre (A): -3.802000 49.36850 13.87600 number of atom coordinates read : 2244 total number of charged atoms : 2110 net assigned charge : 12.51402 assigned positive charge : 328.5036 centred at (gu) : 96.64168 96.53799 87.43648 assigned negative charge : -315.9903 centred at (gu) : 96.42410 96.22480 87.38566 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21571 grid for indexing accessible points = 1.400000 m= 84320 mr = 115340 m= 33243 mr = 67581 m= 9167 mr = 26437 m= 1616 mr = 6746 m= 131 mr = 1072 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 528 time to turn everything in is 0.9400000 number of dielectric boundary points 75786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 16876 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) : 1.972081 object centre at (A) : -3.802000 49.36850 13.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4655241 0.4969849 midg,1,midg; midg,igrid,midg 2.7223589E-02 0.3140043 1,midg,midg; igrid,midg,midg 0.8460879 0.3403948 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.180000 now iterating at: 11:53:05 rms-change max change #iterations 9.711942 399.7795 at 10iterations 5.761403 140.2855 at 20iterations 3.415272 83.19637 at 30iterations 2.013800 47.93572 at 40iterations 1.180530 26.82178 at 50iterations 0.6912746 14.11669 at 60iterations 0.4048591 9.143958 at 70iterations 0.2353281 4.708442 at 80iterations 0.1378117 2.785680 at 90iterations 8.0124781E-02 1.659691 at 100iterations 4.6584357E-02 0.9305420 at 110iterations 2.7126305E-02 0.5123634 at 120iterations 1.5769055E-02 0.3054695 at 130iterations 9.1615831E-03 0.1819344 at 140iterations 5.3246040E-03 0.1008759 at 150iterations 3.0946636E-03 5.6398153E-02 at 160iterations 1.7990354E-03 3.7830353E-02 at 170iterations 1.0486856E-03 1.8459320E-02 at 180iterations finished qdiffx linear iterations at : 11:53:16 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.0486856E-03 1.8459320E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 11:53:17 12.888u 0.218s 0:13.38 97.8% 0+0k 0+0io 0pf+0w