Mon Oct 10 14:01:08 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 14:01:08 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 = 2420 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: 0.6966050 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): -14.05300 37.05200 ymin,ymax (A): -0.5680000 44.28300 zmin,zma (A): -6.713000 43.99200 x,y,z range (A): 51.10500 44.85100 50.70500 scale (grids/A): 0.6966050 object centre (A): 11.49950 21.85750 18.63950 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 91.04843 91.60576 89.99395 assigned negative charge : -366.7416 centred at (gu) : 91.25044 91.66907 89.96483 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7710 nv = 96 ne = 84 npr = 49271 no. pairs analyzed = 49271 no. exposed pairs = 2997 no. arc points = 20565 no. surface atoms = 1006 nbur = 1414 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4299 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3000000 number of dielectric boundary points 3834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1933 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1184526E-08 3.7497784E-08 midg,1,midg; midg,igrid,midg 3.8637396E-08 -6.7932384E-09 1,midg,midg; igrid,midg,midg 9.2581296E-08 -8.5775831E-08 gauss-seidel spectral radius is 0.9892921 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 14:01:09 rms-change max change #iterations 0.2042481 30.51215 at 10iterations 2.4472680E-02 3.569252 at 20iterations 2.9510476E-03 0.3647504 at 30iterations 3.7948776E-04 5.2601576E-02 at 40iterations 6.0272625E-05 8.3384514E-03 at 50iterations finished qdiffx linear iterations at : 14:01:13 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 6.0272625E-05 8.3384514E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 14:01:14 4.618u 0.415s 0:06.01 83.5% 0+0k 0+0io 6pf+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 14:01:14 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 = 2420 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: 2.089815 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): -14.05300 37.05200 ymin,ymax (A): -0.5680000 44.28300 zmin,zma (A): -6.713000 43.99200 x,y,z range (A): 51.10500 44.85100 50.70500 scale (grids/A): 2.089815 object centre (A): 11.49950 21.85750 18.63950 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 93.14487 94.81692 89.98141 assigned negative charge : -366.7416 centred at (gu) : 93.75101 95.00708 89.89440 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20565 grid for indexing accessible points = 1.400000 m= 32519 mr = 56201 m= 6719 mr = 24542 m= 606 mr = 4607 m= 22 mr = 309 m= 0 mr = 6 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.7100000 number of dielectric boundary points 35130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 18072 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) : 0.6966050 object centre at (A) : 11.49950 21.85750 18.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2259569E-02 3.0748164E-02 midg,1,midg; midg,igrid,midg 3.2308910E-02 7.6684874E-04 1,midg,midg; igrid,midg,midg 2.3439575E-02 -7.3094830E-02 gauss-seidel spectral radius is 0.9988329 estimated iterations to convergence 232 setup time was (sec) 1.030000 now iterating at: 14:01:16 rms-change max change #iterations 4.911425 221.3194 at 10iterations 2.430756 82.20197 at 20iterations 1.205028 40.38919 at 30iterations 0.5999496 19.01762 at 40iterations 0.2977948 8.744665 at 50iterations 0.1482413 4.189058 at 60iterations 7.3603719E-02 2.171253 at 70iterations 3.6585987E-02 1.052834 at 80iterations 1.8114744E-02 0.5608315 at 90iterations 9.0019954E-03 0.2753201 at 100iterations 4.4768741E-03 0.1349850 at 110iterations 2.2329164E-03 6.7055225E-02 at 120iterations finished qdiffx linear iterations at : 14:01:26 total time elapsed so far: 11.31000 # loops : 120 mean,max change (kT/e) : 2.2329164E-03 6.7055225E-02 energy calculations done at 11.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 14:01:27 11.491u 0.469s 0:12.70 94.0% 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 14:01:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 3.134722 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): -14.05300 37.05200 ymin,ymax (A): -0.5680000 44.28300 zmin,zma (A): -6.713000 43.99200 x,y,z range (A): 51.10500 44.85100 50.70500 scale (grids/A): 3.134722 object centre (A): 11.49950 21.85750 18.63950 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 370.2410 centred at (gu) : 94.71729 97.22514 89.97208 assigned negative charge : -366.7416 centred at (gu) : 95.62652 97.51043 89.84158 start vw surface at 0.1300000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 186553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20565 grid for indexing accessible points = 1.400000 m= 99552 mr = 135468 m= 42087 mr = 82360 m= 12914 mr = 34631 m= 2516 mr = 10052 m= 294 mr = 1873 m= 16 mr = 204 m= 0 mr = 7 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 1283 time to turn everything in is 2.170000 number of dielectric boundary points 79337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 18224 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) : 2.089815 object centre at (A) : 11.49950 21.85750 18.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2765547 0.1727317 midg,1,midg; midg,igrid,midg 0.2616735 -9.5855817E-02 1,midg,midg; igrid,midg,midg 0.4008619 -0.6511921 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 2.510000 now iterating at: 14:01:30 rms-change max change #iterations 11.07778 521.0703 at 10iterations 6.567432 137.6176 at 20iterations 3.876440 81.68337 at 30iterations 2.288272 43.85236 at 40iterations 1.346081 24.18282 at 50iterations 0.7901229 13.90710 at 60iterations 0.4638169 8.457577 at 70iterations 0.2711346 4.770330 at 80iterations 0.1591299 3.070741 at 90iterations 9.3066148E-02 1.640250 at 100iterations 5.4336868E-02 0.9143817 at 110iterations 3.1853613E-02 0.5609751 at 120iterations 1.8605446E-02 0.3224020 at 130iterations 1.0880928E-02 0.1759129 at 140iterations 6.3666999E-03 0.1072454 at 150iterations 3.7338622E-03 6.5410614E-02 at 160iterations 2.1971501E-03 3.7025452E-02 at 170iterations 1.3011881E-03 2.2350788E-02 at 180iterations finished qdiffx linear iterations at : 14:01:47 total time elapsed so far: 19.50000 # loops : 180 mean,max change (kT/e) : 1.3011881E-03 2.2350788E-02 energy calculations done at 19.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.67000 DelPhi exited at 14:01:48 19.679u 0.466s 0:21.18 95.0% 0+0k 0+0io 0pf+0w