Mon Oct 10 23:15:15 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+sph.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 = amb.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 23:15:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.4959944 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): -18.56000 47.12900 ymin,ymax (A): -19.12700 42.99700 zmin,zma (A): 5.002000 76.77700 x,y,z range (A): 65.68900 62.12400 71.77500 scale (grids/A): 0.4959944 object centre (A): 14.28450 11.93500 40.88950 number of atom coordinates read : 4117 total number of charged atoms : 3959 net assigned charge : 4.000025 assigned positive charge : 620.8298 centred at (gu) : 90.63538 87.85204 92.87679 assigned negative charge : -616.8329 centred at (gu) : 90.68488 87.74560 92.82831 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6362 nv = 96 ne = 84 npr = 81485 no. pairs analyzed = 81485 no. exposed pairs = 5260 no. arc points = 37167 no. surface atoms = 1750 nbur = 2367 mkacc time = 0.1400000 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 = 1.708000 m= 204 mr = 3204 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2800000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3460 ## 583 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1622707E-11 1.8954963E-10 midg,1,midg; midg,igrid,midg -1.7347680E-10 8.4946244E-11 1,midg,midg; igrid,midg,midg 7.3249976E-11 -3.2934253E-11 gauss-seidel spectral radius is 0.9791741 estimated iterations to convergence 57 setup time was (sec) 0.4700000 now iterating at: 23:15:16 rms-change max change #iterations 5.4026760E-02 9.733974 at 10iterations 3.2167675E-03 0.5811882 at 20iterations 2.9882204E-04 4.2499542E-02 at 30iterations 5.6050907E-05 7.1573257E-03 at 40iterations 1.2612842E-05 1.6374588E-03 at 50iterations finished qdiffx linear iterations at : 23:15:19 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.2612842E-05 1.6374588E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 23:15:19 3.455u 0.171s 0:04.20 86.1% 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 Mon Oct 10 2011 at 23:15:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.487983 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): -18.56000 47.12900 ymin,ymax (A): -19.12700 42.99700 zmin,zma (A): 5.002000 76.77700 x,y,z range (A): 65.68900 62.12400 71.77500 scale (grids/A): 1.487983 object centre (A): 14.28450 11.93500 40.88950 number of atom coordinates read : 4117 total number of charged atoms : 3959 net assigned charge : 4.000025 assigned positive charge : 620.8298 centred at (gu) : 91.90485 83.55524 98.62906 assigned negative charge : -616.8329 centred at (gu) : 92.05435 83.23642 98.48459 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37167 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 20216 mr = 48473 m= 1556 mr = 13460 m= 26 mr = 675 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2423 time to turn everything in is 0.3600000 number of dielectric boundary points 31676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 468 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 29387 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) : 0.4959944 object centre at (A) : 14.28450 11.93500 40.88950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6972091E-03 2.5701815E-02 midg,1,midg; midg,igrid,midg -1.0415952E-02 3.4276007E-03 1,midg,midg; igrid,midg,midg 8.7669855E-03 -2.7078078E-03 gauss-seidel spectral radius is 0.9978821 estimated iterations to convergence 173 setup time was (sec) 0.5700000 now iterating at: 23:15:20 rms-change max change #iterations 3.222288 143.2985 at 10iterations 1.252093 41.26886 at 20iterations 0.4870405 17.56675 at 30iterations 0.1896421 9.534596 at 40iterations 7.3880136E-02 2.485832 at 50iterations 2.8825397E-02 1.062045 at 60iterations 1.1250650E-02 0.4074097 at 70iterations 4.3993262E-03 0.1724133 at 80iterations 1.7332607E-03 6.0821533E-02 at 90iterations 6.9027086E-04 2.4269104E-02 at 100iterations 2.8017344E-04 1.0292053E-02 at 110iterations 1.1882914E-04 4.1389465E-03 at 120iterations finished qdiffx linear iterations at : 23:15:27 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.1882914E-04 4.1389465E-03 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 23:15:28 7.637u 0.197s 0:08.31 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 Mon Oct 10 2011 at 23:15:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.231975 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): -18.56000 47.12900 ymin,ymax (A): -19.12700 42.99700 zmin,zma (A): 5.002000 76.77700 x,y,z range (A): 65.68900 62.12400 71.77500 scale (grids/A): 2.231975 object centre (A): 14.28450 11.93500 40.88950 number of atom coordinates read : 4117 total number of charged atoms : 3959 net assigned charge : 4.000025 assigned positive charge : 620.8298 centred at (gu) : 92.85692 80.33238 102.9434 assigned negative charge : -616.8329 centred at (gu) : 93.08154 79.85462 102.7269 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 169097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37167 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 72847 mr = 119598 m= 17957 mr = 56533 m= 2138 mr = 13178 m= 55 mr = 1244 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 7901 time to turn everything in is 0.8500000 number of dielectric boundary points 71532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 31542 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) : 1.487983 object centre at (A) : 14.28450 11.93500 40.88950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6789120E-02 0.5097020 midg,1,midg; midg,igrid,midg -0.2186287 4.9248215E-02 1,midg,midg; igrid,midg,midg 0.1345840 -1.6994581E-02 gauss-seidel spectral radius is 0.9990476 estimated iterations to convergence 256 setup time was (sec) 1.080000 now iterating at: 23:15:29 rms-change max change #iterations 8.909337 345.6242 at 10iterations 4.917410 114.3047 at 20iterations 2.686878 67.21857 at 30iterations 1.459211 33.27843 at 40iterations 0.7895265 18.50410 at 50iterations 0.4257963 10.52289 at 60iterations 0.2288666 5.221127 at 70iterations 0.1230738 2.678783 at 80iterations 6.6128485E-02 1.480644 at 90iterations 3.5413936E-02 0.8303199 at 100iterations 1.8971683E-02 0.4717588 at 110iterations 1.0150685E-02 0.2315199 at 120iterations 5.4424051E-03 0.1173248 at 130iterations 2.9067392E-03 7.1708679E-02 at 140iterations 1.5529906E-03 3.3252716E-02 at 150iterations 8.3192100E-04 1.6661763E-02 at 160iterations 4.4457015E-04 9.5520020E-03 at 170iterations 2.3852983E-04 5.3882599E-03 at 180iterations finished qdiffx linear iterations at : 23:15:40 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 2.3852983E-04 5.3882599E-03 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 23:15:41 12.250u 0.225s 0:12.98 96.0% 0+0k 0+0io 0pf+0w