Tue Oct 11 03:34:50 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 Tue Oct 11 2011 at 03:34:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 !!! WARNING: ASL 118 has a net charge of -0.1000 !!! WARNING: HIR 222 has a net charge of 0.5140 !!! WARNING: ASP 248 has a net charge of -1.5000 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: 0.5634248 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): -8.042000 41.65100 ymin,ymax (A): -29.01700 34.16800 zmin,zma (A): -30.35900 24.57500 x,y,z range (A): 49.69300 63.18501 54.93400 scale (grids/A): 0.5634248 object centre (A): 16.80450 2.575501 -2.892001 number of atom coordinates read : 2748 total number of charged atoms : 2655 net assigned charge : -10.08598 assigned positive charge : 415.4604 centred at (gu) : 90.33310 89.07969 90.66006 assigned negative charge : -425.5473 centred at (gu) : 90.31791 89.07367 90.55479 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5772 nv = 96 ne = 84 npr = 54376 no. pairs analyzed = 54376 no. exposed pairs = 3731 no. arc points = 26803 no. surface atoms = 1235 nbur = 1513 mkacc time = 0.1300000 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 = 1.512000 m= 239 mr = 2858 m= 3 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2646 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1370024E-09 3.2276598E-11 midg,1,midg; midg,igrid,midg -1.6105096E-09 -9.3221464E-10 1,midg,midg; igrid,midg,midg -1.3016389E-09 -1.1274693E-09 gauss-seidel spectral radius is 0.9837397 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 03:34:50 rms-change max change #iterations 8.5485891E-02 15.52218 at 10iterations 6.1462210E-03 1.042525 at 20iterations 4.4271318E-04 6.5711975E-02 at 30iterations 3.3537715E-05 5.3558350E-03 at 40iterations 2.8608149E-06 4.6348572E-04 at 50iterations finished qdiffx linear iterations at : 03:34:53 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.8608149E-06 4.6348572E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:34:54 3.383u 0.159s 0:03.88 90.9% 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 Tue Oct 11 2011 at 03:34:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 !!! WARNING: ASL 118 has a net charge of -0.1000 !!! WARNING: HIR 222 has a net charge of 0.5140 !!! WARNING: ASP 248 has a net charge of -1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.690274 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): -8.042000 41.65100 ymin,ymax (A): -29.01700 34.16800 zmin,zma (A): -30.35900 24.57500 x,y,z range (A): 49.69300 63.18501 54.93400 scale (grids/A): 1.690274 object centre (A): 16.80450 2.575501 -2.892001 number of atom coordinates read : 2748 total number of charged atoms : 2655 net assigned charge : -10.08598 assigned positive charge : 415.4604 centred at (gu) : 90.99880 87.23845 91.97961 assigned negative charge : -425.5473 centred at (gu) : 90.95342 87.22073 91.66393 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26803 grid for indexing accessible points = 1.400000 m= 19700 mr = 41835 m= 2295 mr = 13381 m= 61 mr = 1114 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20532 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) : 0.5634248 object centre at (A) : 16.80450 2.575501 -2.892001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5813544E-02 1.2671876E-02 midg,1,midg; midg,igrid,midg -2.3247212E-02 -2.6783664E-02 1,midg,midg; igrid,midg,midg 1.8011681E-03 -1.3999490E-02 gauss-seidel spectral radius is 0.9983056 estimated iterations to convergence 193 setup time was (sec) 0.8000000 now iterating at: 03:34:55 rms-change max change #iterations 3.516112 150.1774 at 10iterations 1.505450 58.03214 at 20iterations 0.6436762 30.22059 at 30iterations 0.2763135 9.982025 at 40iterations 0.1180828 4.845154 at 50iterations 5.0885987E-02 1.728569 at 60iterations 2.1726388E-02 0.7735929 at 70iterations 9.3561020E-03 0.3683677 at 80iterations 3.9980654E-03 0.1447489 at 90iterations 1.7185027E-03 5.8951855E-02 at 100iterations 7.4047886E-04 2.4852753E-02 at 110iterations 3.1697564E-04 1.1846542E-02 at 120iterations finished qdiffx linear iterations at : 03:35:01 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 3.1697564E-04 1.1846542E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 03:35:02 7.705u 0.187s 0:08.23 95.7% 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 Tue Oct 11 2011 at 03:35:02 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 !!! WARNING: ASL 118 has a net charge of -0.1000 !!! WARNING: HIR 222 has a net charge of 0.5140 !!! WARNING: ASP 248 has a net charge of -1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.535412 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): -8.042000 41.65100 ymin,ymax (A): -29.01700 34.16800 zmin,zma (A): -30.35900 24.57500 x,y,z range (A): 49.69300 63.18501 54.93400 scale (grids/A): 2.535412 object centre (A): 16.80450 2.575501 -2.892001 number of atom coordinates read : 2748 total number of charged atoms : 2655 net assigned charge : -10.08598 assigned positive charge : 415.4604 centred at (gu) : 91.49802 85.85734 92.96924 assigned negative charge : -425.5473 centred at (gu) : 91.43004 85.83086 92.49586 start vw surface at 0.2500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 148086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26803 grid for indexing accessible points = 1.400000 m= 66375 mr = 102926 m= 20254 mr = 51431 m= 3565 mr = 15284 m= 284 mr = 2341 m= 8 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 66463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 21225 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) : 1.690274 object centre at (A) : 16.80450 2.575501 -2.892001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2430711 0.2107196 midg,1,midg; midg,igrid,midg 5.8970049E-02 -0.2880112 1,midg,midg; igrid,midg,midg 6.3612133E-02 -0.2004059 gauss-seidel spectral radius is 0.9991813 estimated iterations to convergence 276 setup time was (sec) 1.540000 now iterating at: 03:35:04 rms-change max change #iterations 8.819041 273.3823 at 10iterations 5.006888 141.6424 at 20iterations 2.829629 72.01424 at 30iterations 1.593421 36.49416 at 40iterations 0.8966582 21.91324 at 50iterations 0.5035058 11.11109 at 60iterations 0.2827247 6.291937 at 70iterations 0.1582528 3.161077 at 80iterations 8.8381931E-02 1.926540 at 90iterations 4.9463093E-02 1.103782 at 100iterations 2.7634507E-02 0.5946999 at 110iterations 1.5422634E-02 0.3210300 at 120iterations 8.6164037E-03 0.1840191 at 130iterations 4.8000044E-03 0.1094644 at 140iterations 2.6779391E-03 5.5553436E-02 at 150iterations 1.4951996E-03 2.9491425E-02 at 160iterations 8.3434233E-04 1.7280579E-02 at 170iterations 4.6469324E-04 9.1018677E-03 at 180iterations finished qdiffx linear iterations at : 03:35:15 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 4.6469324E-04 9.1018677E-03 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 03:35:15 12.654u 0.184s 0:13.43 95.5% 0+0k 0+0io 0pf+0w