Sat Oct 8 17:40:56 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 Sat Oct 8 2011 at 17:40:56 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 = 3534 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5236526 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): -0.9720000 44.52400 ymin,ymax (A): -30.36800 26.16700 zmin,zma (A): 1.420000 69.40400 x,y,z range (A): 45.49600 56.53500 67.98400 scale (grids/A): 0.5236526 object centre (A): 21.77600 -2.100500 35.41200 number of atom coordinates read : 3534 total number of charged atoms : 3387 net assigned charge : -5.771982 assigned positive charge : 535.7321 centred at (gu) : 90.48166 91.76578 90.53717 assigned negative charge : -541.5058 centred at (gu) : 90.44314 91.72430 90.53590 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6122 nv = 96 ne = 84 npr = 72087 no. pairs analyzed = 72087 no. exposed pairs = 4300 no. arc points = 29242 no. surface atoms = 1464 nbur = 2070 mkacc time = 0.1800000 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 = 1.624000 m= 227 mr = 3255 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3271577E-10 -1.6384591E-10 midg,1,midg; midg,igrid,midg -1.8440362E-10 -8.3115606E-12 1,midg,midg; igrid,midg,midg -2.4606028E-10 -1.9612909E-11 gauss-seidel spectral radius is 0.9812505 estimated iterations to convergence 60 setup time was (sec) 0.6800000 now iterating at: 17:40:57 rms-change max change #iterations 6.3682154E-02 11.94611 at 10iterations 3.9092768E-03 0.6425247 at 20iterations 3.7577786E-04 6.6577911E-02 at 30iterations 8.1209000E-05 1.6277313E-02 at 40iterations 2.1350210E-05 4.2839050E-03 at 50iterations finished qdiffx linear iterations at : 17:41:01 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.1350210E-05 4.2839050E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 17:41:01 4.662u 0.398s 0:05.32 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 Sat Oct 8 2011 at 17:41:01 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 = 3534 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.570958 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): -0.9720000 44.52400 ymin,ymax (A): -30.36800 26.16700 zmin,zma (A): 1.420000 69.40400 x,y,z range (A): 45.49600 56.53500 67.98400 scale (grids/A): 1.570958 object centre (A): 21.77600 -2.100500 35.41200 number of atom coordinates read : 3534 total number of charged atoms : 3387 net assigned charge : -5.771982 assigned positive charge : 535.7321 centred at (gu) : 91.44420 95.29638 91.61062 assigned negative charge : -541.5058 centred at (gu) : 91.32887 95.17240 91.60717 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29242 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20554 mr = 48124 m= 1801 mr = 13834 m= 32 mr = 759 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 28770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25589 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) : 0.5236526 object centre at (A) : 21.77600 -2.100500 35.41200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9855214E-03 1.1620775E-02 midg,1,midg; midg,igrid,midg -7.5832102E-03 -1.1086194E-02 1,midg,midg; igrid,midg,midg -4.1810307E-03 8.4944168E-04 gauss-seidel spectral radius is 0.9980753 estimated iterations to convergence 181 setup time was (sec) 0.8800000 now iterating at: 17:41:03 rms-change max change #iterations 3.360523 168.4575 at 10iterations 1.362686 64.86103 at 20iterations 0.5536036 20.30142 at 30iterations 0.2255234 8.408396 at 40iterations 9.2023440E-02 3.239185 at 50iterations 3.7618231E-02 1.418121 at 60iterations 1.5277417E-02 0.6040869 at 70iterations 6.2774266E-03 0.2518187 at 80iterations 2.5923150E-03 9.2618942E-02 at 90iterations 1.0967425E-03 4.2388916E-02 at 100iterations 4.8870832E-04 1.9303322E-02 at 110iterations 2.3569993E-04 8.8424683E-03 at 120iterations finished qdiffx linear iterations at : 17:41:12 total time elapsed so far: 10.25000 # loops : 120 mean,max change (kT/e) : 2.3569993E-04 8.8424683E-03 energy calculations done at 10.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.42000 DelPhi exited at 17:41:12 10.420u 0.455s 0:11.12 97.7% 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 Sat Oct 8 2011 at 17:41:13 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 = 3534 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.356437 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): -0.9720000 44.52400 ymin,ymax (A): -30.36800 26.16700 zmin,zma (A): 1.420000 69.40400 x,y,z range (A): 45.49600 56.53500 67.98400 scale (grids/A): 2.356437 object centre (A): 21.77600 -2.100500 35.41200 number of atom coordinates read : 3534 total number of charged atoms : 3387 net assigned charge : -5.771982 assigned positive charge : 535.7321 centred at (gu) : 92.16609 97.94435 92.41571 assigned negative charge : -541.5058 centred at (gu) : 91.99327 97.75854 92.41072 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 161180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29242 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73584 mr = 118096 m= 18947 mr = 58007 m= 2572 mr = 13810 m= 111 mr = 1442 m= 0 mr = 24 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 65015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 27044 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) : 1.570958 object centre at (A) : 21.77600 -2.100500 35.41200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2636325 7.7943809E-02 midg,1,midg; midg,igrid,midg -0.1089888 -0.1605259 1,midg,midg; igrid,midg,midg -7.5446144E-02 4.2487837E-02 gauss-seidel spectral radius is 0.9991086 estimated iterations to convergence 265 setup time was (sec) 1.710000 now iterating at: 17:41:15 rms-change max change #iterations 9.020765 298.9690 at 10iterations 5.036578 139.6010 at 20iterations 2.792919 66.28427 at 30iterations 1.540096 34.86919 at 40iterations 0.8464668 17.41518 at 50iterations 0.4623130 10.31405 at 60iterations 0.2533303 5.745275 at 70iterations 0.1382573 2.691044 at 80iterations 7.5384989E-02 1.544118 at 90iterations 4.1178219E-02 0.8617363 at 100iterations 2.2472799E-02 0.4530220 at 110iterations 1.2243750E-02 0.2464619 at 120iterations 6.6716457E-03 0.1289673 at 130iterations 3.6330391E-03 7.3933601E-02 at 140iterations 1.9790735E-03 4.0915012E-02 at 150iterations 1.0783846E-03 2.1785021E-02 at 160iterations 5.9360603E-04 1.3309479E-02 at 170iterations 3.2726277E-04 6.7024231E-03 at 180iterations finished qdiffx linear iterations at : 17:41:30 total time elapsed so far: 17.34000 # loops : 180 mean,max change (kT/e) : 3.2726277E-04 6.7024231E-03 energy calculations done at 17.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.51000 DelPhi exited at 17:41:31 17.516u 0.493s 0:18.29 98.4% 0+0k 0+0io 0pf+0w