Sun Oct 9 15:06:40 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 Sun Oct 9 2011 at 15:06:40 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5668 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 448 has a net charge of 0.5140 !!! WARNING: HIR 661 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.5052655 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): -17.64800 52.81000 ymin,ymax (A): 98.53300 167.9090 zmin,zma (A): -34.66100 31.55000 x,y,z range (A): 70.45800 69.37600 66.21101 scale (grids/A): 0.5052655 object centre (A): 17.58100 133.2210 -1.555501 number of atom coordinates read : 5668 total number of charged atoms : 5488 net assigned charge : -5.051957 assigned positive charge : 873.2144 centred at (gu) : 89.96304 88.92892 88.75323 assigned negative charge : -878.2737 centred at (gu) : 89.95155 88.99868 88.72651 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 8802 nv = 96 ne = 84 npr = 117257 no. pairs analyzed = 117257 no. exposed pairs = 6461 no. arc points = 43989 no. surface atoms = 2182 nbur = 3486 mkacc time = 0.2800000 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 = 1.708000 m= 306 mr = 4909 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.5700000 number of dielectric boundary points 4195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 11887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7457767E-10 6.5115773E-12 midg,1,midg; midg,igrid,midg 1.5780964E-10 -1.7699912E-10 1,midg,midg; igrid,midg,midg -8.7306676E-11 -2.8110242E-11 gauss-seidel spectral radius is 0.9800146 estimated iterations to convergence 58 setup time was (sec) 0.8000000 now iterating at: 15:06:41 rms-change max change #iterations 7.1377516E-02 11.24409 at 10iterations 5.1738871E-03 0.7303009 at 20iterations 8.9558563E-04 0.1534042 at 30iterations 2.2552215E-04 3.6674500E-02 at 40iterations 5.8539379E-05 9.3803406E-03 at 50iterations finished qdiffx linear iterations at : 15:06:44 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.8539379E-05 9.3803406E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:06:44 3.604u 0.149s 0:04.03 92.8% 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 Sun Oct 9 2011 at 15:06:44 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5668 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 448 has a net charge of 0.5140 !!! WARNING: HIR 661 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.515797 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): -17.64800 52.81000 ymin,ymax (A): 98.53300 167.9090 zmin,zma (A): -34.66100 31.55000 x,y,z range (A): 70.45800 69.37600 66.21101 scale (grids/A): 1.515797 object centre (A): 17.58100 133.2210 -1.555501 number of atom coordinates read : 5668 total number of charged atoms : 5488 net assigned charge : -5.051957 assigned positive charge : 873.2144 centred at (gu) : 89.88767 86.78514 86.25803 assigned negative charge : -878.2737 centred at (gu) : 89.85477 86.99552 86.17913 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 100873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43989 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28693 mr = 72063 m= 2391 mr = 19810 m= 44 mr = 1001 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2947 time to turn everything in is 0.7200000 number of dielectric boundary points 39127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 610 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 41043 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) : 0.5052655 object centre at (A) : 17.58100 133.2210 -1.555501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6199447E-03 -6.2080738E-03 midg,1,midg; midg,igrid,midg 2.1161927E-02 -1.0423475E-02 1,midg,midg; igrid,midg,midg -2.4304414E-02 -1.0826256E-02 gauss-seidel spectral radius is 0.9981185 estimated iterations to convergence 183 setup time was (sec) 1.010000 now iterating at: 15:06:46 rms-change max change #iterations 4.173188 156.1450 at 10iterations 1.715472 49.51255 at 20iterations 0.7065383 23.66868 at 30iterations 0.2903245 9.350266 at 40iterations 0.1202107 3.583601 at 50iterations 4.9539879E-02 1.636372 at 60iterations 2.0493148E-02 0.6560822 at 70iterations 8.5481964E-03 0.2579937 at 80iterations 3.6075483E-03 0.1180573 at 90iterations 1.5497496E-03 4.5219421E-02 at 100iterations 6.8648183E-04 2.3637772E-02 at 110iterations 3.2113964E-04 1.1581421E-02 at 120iterations finished qdiffx linear iterations at : 15:06:52 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.2113964E-04 1.1581421E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 15:06:53 7.907u 0.196s 0:08.41 96.1% 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 Sun Oct 9 2011 at 15:06:53 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5668 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 448 has a net charge of 0.5140 !!! WARNING: HIR 661 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.273695 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): -17.64800 52.81000 ymin,ymax (A): 98.53300 167.9090 zmin,zma (A): -34.66100 31.55000 x,y,z range (A): 70.45800 69.37600 66.21101 scale (grids/A): 2.273695 object centre (A): 17.58100 133.2210 -1.555501 number of atom coordinates read : 5668 total number of charged atoms : 5488 net assigned charge : -5.051957 assigned positive charge : 873.2144 centred at (gu) : 89.83081 85.17731 84.38660 assigned negative charge : -878.2737 centred at (gu) : 89.78229 85.49316 84.26852 start vw surface at 0.2400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 235501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43989 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 104556 mr = 176428 m= 25954 mr = 83391 m= 3448 mr = 19258 m= 136 mr = 2119 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 9945 time to turn everything in is 1.750000 number of dielectric boundary points 88365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 43778 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) : 1.515797 object centre at (A) : 17.58100 133.2210 -1.555501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2606651 -0.1737585 midg,1,midg; midg,igrid,midg 0.5036191 -0.1979048 1,midg,midg; igrid,midg,midg -0.3583843 -0.2548678 gauss-seidel spectral radius is 0.9991677 estimated iterations to convergence 274 setup time was (sec) 2.060000 now iterating at: 15:06:55 rms-change max change #iterations 11.18307 265.9758 at 10iterations 6.377599 131.3225 at 20iterations 3.607831 74.52017 at 30iterations 2.032728 41.69310 at 40iterations 1.142232 27.04433 at 50iterations 0.6398010 12.62269 at 60iterations 0.3580613 7.395599 at 70iterations 0.1998553 3.880392 at 80iterations 0.1115498 2.152878 at 90iterations 6.2178332E-02 1.247483 at 100iterations 3.4708798E-02 0.5963669 at 110iterations 1.9338612E-02 0.3531303 at 120iterations 1.0770394E-02 0.1934204 at 130iterations 5.9980098E-03 0.1239796 at 140iterations 3.3457787E-03 6.0036659E-02 at 150iterations 1.8640731E-03 3.3933640E-02 at 160iterations 1.0433800E-03 1.7429352E-02 at 170iterations 5.8459037E-04 9.9525452E-03 at 180iterations finished qdiffx linear iterations at : 15:07:06 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 5.8459037E-04 9.9525452E-03 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 15:07:06 13.155u 0.185s 0:13.64 97.7% 0+0k 0+0io 0pf+0w