Mon Oct 10 09:19:34 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 Mon Oct 10 2011 at 09:19:34 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2915 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5803055 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): -17.82800 33.85600 ymin,ymax (A): -58.79200 -1.199000 zmin,zma (A): -1.368000 59.97900 x,y,z range (A): 51.68400 57.59300 61.34700 scale (grids/A): 0.5803055 object centre (A): 8.013999 -29.99550 29.30550 number of atom coordinates read : 2915 total number of charged atoms : 2763 net assigned charge : 8.000022 assigned positive charge : 425.9498 centred at (gu) : 88.91026 87.94601 87.62312 assigned negative charge : -417.9503 centred at (gu) : 88.97502 87.77234 87.52326 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6639 nv = 96 ne = 84 npr = 56537 no. pairs analyzed = 56537 no. exposed pairs = 4362 no. arc points = 32632 no. surface atoms = 1444 nbur = 1471 mkacc time = 0.1000000 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= 355 mr = 2862 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3124 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6443163E-10 2.2608380E-09 midg,1,midg; midg,igrid,midg -2.9980836E-09 3.3410916E-09 1,midg,midg; igrid,midg,midg 4.1174255E-09 4.2338000E-10 gauss-seidel spectral radius is 0.9846887 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 09:19:35 rms-change max change #iterations 9.7396627E-02 18.55006 at 10iterations 7.2775623E-03 1.143032 at 20iterations 5.8110355E-04 9.7625732E-02 at 30iterations 5.3602722E-05 7.7371597E-03 at 40iterations 7.8202047E-06 9.2124939E-04 at 50iterations finished qdiffx linear iterations at : 09:19:38 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 7.8202047E-06 9.2124939E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 09:19:38 3.428u 0.182s 0:03.87 93.0% 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 09:19:38 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2915 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.740916 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): -17.82800 33.85600 ymin,ymax (A): -58.79200 -1.199000 zmin,zma (A): -1.368000 59.97900 x,y,z range (A): 51.68400 57.59300 61.34700 scale (grids/A): 1.740916 object centre (A): 8.013999 -29.99550 29.30550 number of atom coordinates read : 2915 total number of charged atoms : 2763 net assigned charge : 8.000022 assigned positive charge : 425.9498 centred at (gu) : 86.73025 83.83766 82.86909 assigned negative charge : -417.9503 centred at (gu) : 86.92471 83.31682 82.56943 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32632 grid for indexing accessible points = 1.400000 m= 22148 mr = 42840 m= 2975 mr = 14003 m= 136 mr = 1308 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 38058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21464 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) : 0.5803055 object centre at (A) : 8.013999 -29.99550 29.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2098663E-03 4.6813996E-03 midg,1,midg; midg,igrid,midg 8.5748322E-03 2.9709028E-02 1,midg,midg; igrid,midg,midg 1.0590315E-02 1.4406294E-02 gauss-seidel spectral radius is 0.9984282 estimated iterations to convergence 200 setup time was (sec) 0.5800000 now iterating at: 09:19:39 rms-change max change #iterations 3.728107 188.1874 at 10iterations 1.643756 55.72815 at 20iterations 0.7255775 26.00907 at 30iterations 0.3215202 10.64868 at 40iterations 0.1419178 4.938412 at 50iterations 6.2966123E-02 2.242031 at 60iterations 2.7740881E-02 0.9426708 at 70iterations 1.2323638E-02 0.4684105 at 80iterations 5.4508406E-03 0.2062676 at 90iterations 2.4051750E-03 8.5538864E-02 at 100iterations 1.0634980E-03 3.9295197E-02 at 110iterations 4.6969022E-04 1.5045166E-02 at 120iterations finished qdiffx linear iterations at : 09:19:46 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 4.6969022E-04 1.5045166E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 09:19:46 7.903u 0.190s 0:08.42 96.0% 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 09:19:47 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2915 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.611375 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): -17.82800 33.85600 ymin,ymax (A): -58.79200 -1.199000 zmin,zma (A): -1.368000 59.97900 x,y,z range (A): 51.68400 57.59300 61.34700 scale (grids/A): 2.611375 object centre (A): 8.013999 -29.99550 29.30550 number of atom coordinates read : 2915 total number of charged atoms : 2763 net assigned charge : 8.000022 assigned positive charge : 425.9498 centred at (gu) : 85.09514 80.75642 79.30350 assigned negative charge : -417.9503 centred at (gu) : 85.38701 79.97517 78.85406 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32632 grid for indexing accessible points = 1.400000 m= 72575 mr = 105658 m= 23934 mr = 53877 m= 4758 mr = 16899 m= 513 mr = 2851 m= 15 mr = 203 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 85869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 22090 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) : 1.740916 object centre at (A) : 8.013999 -29.99550 29.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7458057E-02 4.6026021E-02 midg,1,midg; midg,igrid,midg 0.2035354 0.3574012 1,midg,midg; igrid,midg,midg 4.0512603E-02 0.1767170 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.130000 now iterating at: 09:19:48 rms-change max change #iterations 9.536834 387.2455 at 10iterations 5.707107 171.4831 at 20iterations 3.357331 87.92432 at 30iterations 1.957481 57.91282 at 40iterations 1.132972 29.70790 at 50iterations 0.6538830 18.46657 at 60iterations 0.3767074 8.659336 at 70iterations 0.2167211 4.654466 at 80iterations 0.1242226 2.903978 at 90iterations 7.1269810E-02 1.571152 at 100iterations 4.0650200E-02 0.9299622 at 110iterations 2.3219114E-02 0.5313091 at 120iterations 1.3226012E-02 0.2850189 at 130iterations 7.5533767E-03 0.1542516 at 140iterations 4.3059736E-03 9.9898219E-02 at 150iterations 2.4493332E-03 5.1645279E-02 at 160iterations 1.3948663E-03 2.9161453E-02 at 170iterations 7.9503679E-04 1.5552521E-02 at 180iterations finished qdiffx linear iterations at : 09:19:59 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 7.9503679E-04 1.5552521E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 09:20:00 12.873u 0.213s 0:13.35 97.9% 0+0k 0+0io 0pf+0w