Mon Oct 10 17:14:58 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 17:14:58 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: 358 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2958 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 0.5371720 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): -8.330000 38.31100 ymin,ymax (A): -9.299000 43.53600 zmin,zma (A): -3.478000 62.79500 x,y,z range (A): 46.64100 52.83500 66.27300 scale (grids/A): 0.5371720 object centre (A): 14.99050 17.11850 29.65850 number of atom coordinates read : 2958 total number of charged atoms : 2781 net assigned charge : 1.806032 assigned positive charge : 438.3092 centred at (gu) : 90.83474 89.45927 89.20217 assigned negative charge : -436.5043 centred at (gu) : 90.81160 89.39931 89.28664 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5538 nv = 96 ne = 84 npr = 58703 no. pairs analyzed = 58703 no. exposed pairs = 4016 no. arc points = 28316 no. surface atoms = 1338 nbur = 1620 mkacc time = 0.2000000 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 = 1.596000 m= 242 mr = 2724 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2788 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7247 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7125110E-10 -2.6193869E-10 midg,1,midg; midg,igrid,midg -2.3638866E-10 3.0888267E-10 1,midg,midg; igrid,midg,midg -2.5019738E-11 2.2716973E-10 gauss-seidel spectral radius is 0.9821420 estimated iterations to convergence 62 setup time was (sec) 0.7500000 now iterating at: 17:14:59 rms-change max change #iterations 6.7183979E-02 14.14066 at 10iterations 4.4025499E-03 0.7707205 at 20iterations 3.7003448E-04 7.4501038E-02 at 30iterations 5.5626122E-05 1.0888100E-02 at 40iterations 1.1228803E-05 2.2706985E-03 at 50iterations finished qdiffx linear iterations at : 17:15:03 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.1228803E-05 2.2706985E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 17:15:03 4.701u 0.410s 0:05.53 92.4% 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 17:15:03 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: 358 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2958 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.611516 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): -8.330000 38.31100 ymin,ymax (A): -9.299000 43.53600 zmin,zma (A): -3.478000 62.79500 x,y,z range (A): 46.64100 52.83500 66.27300 scale (grids/A): 1.611516 object centre (A): 14.99050 17.11850 29.65850 number of atom coordinates read : 2958 total number of charged atoms : 2781 net assigned charge : 1.806032 assigned positive charge : 438.3092 centred at (gu) : 92.50370 88.37688 87.60605 assigned negative charge : -436.5043 centred at (gu) : 92.43465 88.19782 87.85961 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 61513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28316 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18151 mr = 40310 m= 1819 mr = 12085 m= 56 mr = 817 m= 0 mr = 5 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 28322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21223 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) : 0.5371720 object centre at (A) : 14.99050 17.11850 29.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5300314E-02 8.7256329E-03 midg,1,midg; midg,igrid,midg -1.0169703E-02 -2.7150502E-03 1,midg,midg; igrid,midg,midg -4.5369446E-04 1.0819122E-03 gauss-seidel spectral radius is 0.9981391 estimated iterations to convergence 184 setup time was (sec) 0.9600000 now iterating at: 17:15:05 rms-change max change #iterations 3.190633 147.3824 at 10iterations 1.313240 60.55523 at 20iterations 0.5403199 21.85514 at 30iterations 0.2223484 8.983452 at 40iterations 9.1697708E-02 3.634098 at 50iterations 3.7747942E-02 1.379848 at 60iterations 1.5611771E-02 0.5979042 at 70iterations 6.4318683E-03 0.2363243 at 80iterations 2.6661491E-03 0.1068878 at 90iterations 1.1069044E-03 4.9293518E-02 at 100iterations 4.6327218E-04 1.7616272E-02 at 110iterations 1.9669539E-04 7.8735352E-03 at 120iterations finished qdiffx linear iterations at : 17:15:14 total time elapsed so far: 10.31000 # loops : 120 mean,max change (kT/e) : 1.9669539E-04 7.8735352E-03 energy calculations done at 10.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 17:15:15 10.547u 0.443s 0:11.56 94.9% 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 Mon Oct 10 2011 at 17:15:15 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: 358 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2958 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.417274 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): -8.330000 38.31100 ymin,ymax (A): -9.299000 43.53600 zmin,zma (A): -3.478000 62.79500 x,y,z range (A): 46.64100 52.83500 66.27300 scale (grids/A): 2.417274 object centre (A): 14.99050 17.11850 29.65850 number of atom coordinates read : 2958 total number of charged atoms : 2781 net assigned charge : 1.806032 assigned positive charge : 438.3092 centred at (gu) : 93.75542 87.56528 86.40887 assigned negative charge : -436.5043 centred at (gu) : 93.65176 87.29662 86.78915 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 142898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28316 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63660 mr = 99329 m= 17329 mr = 49194 m= 2725 mr = 12598 m= 204 mr = 1690 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 63930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 22209 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) : 1.611516 object centre at (A) : 14.99050 17.11850 29.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1641747 0.2697028 midg,1,midg; midg,igrid,midg -0.1316841 -7.3228993E-02 1,midg,midg; igrid,midg,midg 3.2433777E-03 1.0877198E-02 gauss-seidel spectral radius is 0.9991292 estimated iterations to convergence 268 setup time was (sec) 1.930000 now iterating at: 17:15:17 rms-change max change #iterations 8.471102 298.9330 at 10iterations 4.786239 149.5619 at 20iterations 2.676021 63.40033 at 30iterations 1.488737 35.42787 at 40iterations 0.8232128 22.03151 at 50iterations 0.4532326 12.16529 at 60iterations 0.2491919 6.952845 at 70iterations 0.1371661 3.064308 at 80iterations 7.5419821E-02 1.695694 at 90iterations 4.1356158E-02 0.9442737 at 100iterations 2.2706609E-02 0.4804611 at 110iterations 1.2465598E-02 0.2729214 at 120iterations 6.8275491E-03 0.1478920 at 130iterations 3.7381060E-03 8.0144882E-02 at 140iterations 2.0489031E-03 4.7538757E-02 at 150iterations 1.1273905E-03 2.2844315E-02 at 160iterations 6.2021177E-04 1.5331268E-02 at 170iterations 3.4187891E-04 8.5430145E-03 at 180iterations finished qdiffx linear iterations at : 17:15:33 total time elapsed so far: 18.06000 # loops : 180 mean,max change (kT/e) : 3.4187891E-04 8.5430145E-03 energy calculations done at 18.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.27000 DelPhi exited at 17:15:34 18.273u 0.502s 0:19.56 95.9% 0+0k 0+0io 0pf+0w