Tue Oct 11 08:33:14 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+sph.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 = amb.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 08:33:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2079 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6973829 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): -19.26800 23.86200 ymin,ymax (A): -12.39200 28.74400 zmin,zma (A): -2.923000 48.12500 x,y,z range (A): 43.13000 41.13600 51.04800 scale (grids/A): 0.6973829 object centre (A): 2.297000 8.176001 22.60100 number of atom coordinates read : 2079 total number of charged atoms : 1962 net assigned charge : 6.500009 assigned positive charge : 317.7640 centred at (gu) : 89.81664 89.70925 90.56918 assigned negative charge : -311.2642 centred at (gu) : 89.69936 89.72822 90.63580 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6885 nv = 96 ne = 84 npr = 41247 no. pairs analyzed = 41247 no. exposed pairs = 2529 no. arc points = 17241 no. surface atoms = 860 nbur = 1219 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 3969 m= 2 mr = 79 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 0.2800000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1651 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7706 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2102451E-08 1.8773980E-08 midg,1,midg; midg,igrid,midg 5.3730961E-08 3.3994112E-08 1,midg,midg; igrid,midg,midg -3.4832512E-09 8.5759304E-08 gauss-seidel spectral radius is 0.9892844 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 08:33:15 rms-change max change #iterations 0.1869241 26.22736 at 10iterations 2.2016449E-02 3.327178 at 20iterations 2.8569563E-03 0.4293900 at 30iterations 4.5584192E-04 6.2057495E-02 at 40iterations 1.0754380E-04 1.4355659E-02 at 50iterations finished qdiffx linear iterations at : 08:33:19 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 1.0754380E-04 1.4355659E-02 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 08:33:19 4.626u 0.368s 0:05.29 94.1% 0+0k 0+0io 6pf+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 08:33:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2079 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: 2.092149 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): -19.26800 23.86200 ymin,ymax (A): -12.39200 28.74400 zmin,zma (A): -2.923000 48.12500 x,y,z range (A): 43.13000 41.13600 51.04800 scale (grids/A): 2.092149 object centre (A): 2.297000 8.176001 22.60100 number of atom coordinates read : 2079 total number of charged atoms : 1962 net assigned charge : 6.500009 assigned positive charge : 317.7640 centred at (gu) : 89.44971 89.12771 91.70757 assigned negative charge : -311.2642 centred at (gu) : 89.09822 89.18474 91.90755 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17241 grid for indexing accessible points = 1.400000 m= 29816 mr = 52356 m= 5581 mr = 22751 m= 460 mr = 3662 m= 3 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 2.860000 number of grid points assigned charge 15569 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) : 0.6973829 object centre at (A) : 2.297000 8.176001 22.60100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2577243E-02 5.2966550E-02 midg,1,midg; midg,igrid,midg 2.5052795E-02 8.8037886E-03 1,midg,midg; igrid,midg,midg 9.5437663E-03 3.2878924E-02 gauss-seidel spectral radius is 0.9988008 estimated iterations to convergence 229 setup time was (sec) 3.080000 now iterating at: 08:33:23 rms-change max change #iterations 4.522603 220.6078 at 10iterations 2.208048 72.86947 at 20iterations 1.087724 36.63740 at 30iterations 0.5377811 17.55530 at 40iterations 0.2637810 8.376132 at 50iterations 0.1301523 4.422615 at 60iterations 6.4193122E-02 2.192271 at 70iterations 3.1703450E-02 0.9102898 at 80iterations 1.5637344E-02 0.5385665 at 90iterations 7.7812495E-03 0.2308192 at 100iterations 3.8722213E-03 0.1246948 at 110iterations 1.9681917E-03 5.8278084E-02 at 120iterations finished qdiffx linear iterations at : 08:33:32 total time elapsed so far: 12.56000 # loops : 120 mean,max change (kT/e) : 1.9681917E-03 5.8278084E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 08:33:33 12.731u 0.429s 0:13.47 97.6% 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 08:33:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2079 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.138223 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): -19.26800 23.86200 ymin,ymax (A): -12.39200 28.74400 zmin,zma (A): -2.923000 48.12500 x,y,z range (A): 43.13000 41.13600 51.04800 scale (grids/A): 3.138223 object centre (A): 2.297000 8.176001 22.60100 number of atom coordinates read : 2079 total number of charged atoms : 1962 net assigned charge : 6.500009 assigned positive charge : 317.7640 centred at (gu) : 89.17461 88.69161 92.56125 assigned negative charge : -311.2642 centred at (gu) : 88.64735 88.77711 92.86125 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 169263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17241 grid for indexing accessible points = 1.400000 m= 92592 mr = 126254 m= 37620 mr = 77136 m= 10464 mr = 30991 m= 1982 mr = 8039 m= 192 mr = 1442 m= 3 mr = 110 m= 0 mr = 2 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 68142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 15688 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) : 2.092149 object centre at (A) : 2.297000 8.176001 22.60100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2140554 0.6403262 midg,1,midg; midg,igrid,midg 0.1885370 5.5761032E-02 1,midg,midg; igrid,midg,midg 0.2278863 0.2959352 gauss-seidel spectral radius is 0.9992859 estimated iterations to convergence 295 setup time was (sec) 2.260000 now iterating at: 08:33:35 rms-change max change #iterations 10.08946 366.8304 at 10iterations 5.972551 125.0602 at 20iterations 3.517796 75.35471 at 30iterations 2.066134 41.94320 at 40iterations 1.214688 22.51528 at 50iterations 0.7107878 13.12535 at 60iterations 0.4169314 9.069210 at 70iterations 0.2432862 4.788614 at 80iterations 0.1419752 2.461155 at 90iterations 8.3195500E-02 1.538502 at 100iterations 4.8561163E-02 0.8151038 at 110iterations 2.8464442E-02 0.4946022 at 120iterations 1.6706731E-02 0.2933273 at 130iterations 9.8843249E-03 0.1751480 at 140iterations 5.9515657E-03 0.1166954 at 150iterations 3.6671490E-03 7.3760986E-02 at 160iterations 2.3551839E-03 4.5325279E-02 at 170iterations 1.5962549E-03 2.9758453E-02 at 180iterations finished qdiffx linear iterations at : 08:33:51 total time elapsed so far: 18.29000 # loops : 180 mean,max change (kT/e) : 1.5962549E-03 2.9758453E-02 energy calculations done at 18.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.46000 DelPhi exited at 08:33:52 18.465u 0.476s 0:19.23 98.4% 0+0k 0+0io 0pf+0w