Mon Oct 10 19:06:19 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 19:06:19 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 !!! WARNING: GLM 277 has a net charge of -0.0940 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 0.6492677 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): -56.37200 -3.614000 ymin,ymax (A): -3.474000 49.14900 zmin,zma (A): -26.85400 27.97700 x,y,z range (A): 52.75800 52.62300 54.83100 scale (grids/A): 0.6492677 object centre (A): -29.99300 22.83750 0.5614996 number of atom coordinates read : 2311 total number of charged atoms : 2172 net assigned charge : -7.9993814E-02 assigned positive charge : 338.1425 centred at (gu) : 89.98948 88.49269 89.23714 assigned negative charge : -338.2231 centred at (gu) : 90.00066 88.46416 89.27930 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6680 nv = 96 ne = 84 npr = 47272 no. pairs analyzed = 47272 no. exposed pairs = 2931 no. arc points = 20290 no. surface atoms = 994 nbur = 1317 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3638 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3600000 number of dielectric boundary points 3376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1904 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7759 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2801715E-09 -4.7905488E-09 midg,1,midg; midg,igrid,midg -5.3481388E-09 2.5809610E-09 1,midg,midg; igrid,midg,midg 1.3200881E-09 -1.5858503E-09 gauss-seidel spectral radius is 0.9876860 estimated iterations to convergence 74 setup time was (sec) 0.7000000 now iterating at: 19:06:20 rms-change max change #iterations 0.1457618 23.99442 at 10iterations 1.4578643E-02 2.369209 at 20iterations 1.5438736E-03 0.2182955 at 30iterations 1.6716265E-04 2.6277065E-02 at 40iterations 2.1643868E-05 3.4675598E-03 at 50iterations finished qdiffx linear iterations at : 19:06:24 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 2.1643868E-05 3.4675598E-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) 4.670000 DelPhi exited at 19:06:25 4.671u 0.394s 0:05.39 93.8% 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 19:06:25 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 !!! WARNING: GLM 277 has a net charge of -0.0940 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 1.947803 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): -56.37200 -3.614000 ymin,ymax (A): -3.474000 49.14900 zmin,zma (A): -26.85400 27.97700 x,y,z range (A): 52.75800 52.62300 54.83100 scale (grids/A): 1.947803 object centre (A): -29.99300 22.83750 0.5614996 number of atom coordinates read : 2311 total number of charged atoms : 2172 net assigned charge : -7.9993814E-02 assigned positive charge : 338.1425 centred at (gu) : 89.96812 85.47779 87.71116 assigned negative charge : -338.2231 centred at (gu) : 90.00208 85.39243 87.83806 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 71819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20290 grid for indexing accessible points = 1.400000 m= 26147 mr = 49865 m= 4742 mr = 19098 m= 390 mr = 3024 m= 4 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 754 time to turn everything in is 0.7600000 number of dielectric boundary points 30949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 17153 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) : 0.6492677 object centre at (A) : -29.99300 22.83750 0.5614996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9243720E-02 1.1501462E-02 midg,1,midg; midg,igrid,midg -7.3018542E-04 1.9205127E-02 1,midg,midg; igrid,midg,midg -3.7595857E-02 -1.3120894E-02 gauss-seidel spectral radius is 0.9986664 estimated iterations to convergence 217 setup time was (sec) 1.100000 now iterating at: 19:06:26 rms-change max change #iterations 4.147316 196.1032 at 10iterations 1.956803 67.76290 at 20iterations 0.9215195 32.07912 at 30iterations 0.4359177 14.45291 at 40iterations 0.2057960 6.418323 at 50iterations 9.7177230E-02 3.157890 at 60iterations 4.6006136E-02 1.515253 at 70iterations 2.1687290E-02 0.7516799 at 80iterations 1.0244231E-02 0.3173037 at 90iterations 4.8635649E-03 0.1612549 at 100iterations 2.2999586E-03 8.1546307E-02 at 110iterations 1.0862394E-03 3.2955170E-02 at 120iterations finished qdiffx linear iterations at : 19:06:38 total time elapsed so far: 12.82000 # loops : 120 mean,max change (kT/e) : 1.0862394E-03 3.2955170E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 19:06:39 13.050u 0.429s 0:14.00 96.2% 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 19:06:39 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2311 !!! WARNING: GLM 277 has a net charge of -0.0940 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 2.921705 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): -56.37200 -3.614000 ymin,ymax (A): -3.474000 49.14900 zmin,zma (A): -26.85400 27.97700 x,y,z range (A): 52.75800 52.62300 54.83100 scale (grids/A): 2.921705 object centre (A): -29.99300 22.83750 0.5614996 number of atom coordinates read : 2311 total number of charged atoms : 2172 net assigned charge : -7.9993814E-02 assigned positive charge : 338.1425 centred at (gu) : 89.95221 83.21677 86.56660 assigned negative charge : -338.2231 centred at (gu) : 90.00322 83.08871 86.75701 start vw surface at 0.1400000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 166364 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20290 grid for indexing accessible points = 1.400000 m= 83535 mr = 120951 m= 31810 mr = 68234 m= 8700 mr = 25385 m= 1650 mr = 6568 m= 160 mr = 1136 m= 6 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 2544 time to turn everything in is 1.990000 number of dielectric boundary points 69848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 17375 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) : 1.947803 object centre at (A) : -29.99300 22.83750 0.5614996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6319457 0.1162735 midg,1,midg; midg,igrid,midg 0.3062968 0.1690833 1,midg,midg; igrid,midg,midg -0.4088882 -0.2088608 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 2.360000 now iterating at: 19:06:41 rms-change max change #iterations 9.725605 385.3572 at 10iterations 5.759262 162.8662 at 20iterations 3.399693 77.51378 at 30iterations 1.994160 49.32991 at 40iterations 1.163457 22.43922 at 50iterations 0.6781068 12.88464 at 60iterations 0.3940929 8.655197 at 70iterations 0.2282800 4.205643 at 80iterations 0.1322020 2.752691 at 90iterations 7.6712951E-02 1.588061 at 100iterations 4.4357583E-02 0.8381624 at 110iterations 2.5550226E-02 0.4580460 at 120iterations 1.4773699E-02 0.2792130 at 130iterations 8.5194865E-03 0.1632631 at 140iterations 4.9219872E-03 9.5041513E-02 at 150iterations 2.8445665E-03 5.1305771E-02 at 160iterations 1.6473959E-03 3.3897400E-02 at 170iterations 9.5929252E-04 1.7810166E-02 at 180iterations finished qdiffx linear iterations at : 19:06:57 total time elapsed so far: 18.13000 # loops : 180 mean,max change (kT/e) : 9.5929252E-04 1.7810166E-02 energy calculations done at 18.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.35000 DelPhi exited at 19:06:58 18.350u 0.465s 0:19.31 97.4% 0+0k 0+0io 0pf+0w