Mon Oct 10 09:44:57 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 Mon Oct 10 2011 at 09:44:57 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 = 2923 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: 0.5729829 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): 113.2480 175.3790 ymin,ymax (A): -43.69800 10.17100 zmin,zma (A): 45.89500 101.6520 x,y,z range (A): 62.13100 53.86900 55.75700 scale (grids/A): 0.5729829 object centre (A): 144.3135 -16.76350 73.77350 number of atom coordinates read : 2923 total number of charged atoms : 2770 net assigned charge : 8.000016 assigned positive charge : 426.8099 centred at (gu) : 89.40961 89.43479 89.77879 assigned negative charge : -418.8103 centred at (gu) : 89.44047 89.49493 89.61857 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6422 nv = 96 ne = 84 npr = 56500 no. pairs analyzed = 56500 no. exposed pairs = 4577 no. arc points = 33636 no. surface atoms = 1499 nbur = 1424 mkacc time = 0.1300000 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 = 1.512000 m= 321 mr = 2677 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3303 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3887617E-09 3.7401491E-09 midg,1,midg; midg,igrid,midg 2.6765083E-09 3.3260164E-10 1,midg,midg; igrid,midg,midg 2.1448316E-09 7.5202561E-10 gauss-seidel spectral radius is 0.9842988 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 09:44:58 rms-change max change #iterations 8.9307897E-02 15.80336 at 10iterations 6.5946830E-03 1.058250 at 20iterations 4.9307512E-04 7.4905396E-02 at 30iterations 4.1804342E-05 5.7907104E-03 at 40iterations 5.6196677E-06 7.3814392E-04 at 50iterations finished qdiffx linear iterations at : 09:45:01 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.6196677E-06 7.3814392E-04 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 09:45:02 3.606u 0.163s 0:04.24 88.6% 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 Mon Oct 10 2011 at 09:45:02 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 = 2923 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: 1.718949 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): 113.2480 175.3790 ymin,ymax (A): -43.69800 10.17100 zmin,zma (A): 45.89500 101.6520 x,y,z range (A): 62.13100 53.86900 55.75700 scale (grids/A): 1.718949 object centre (A): 144.3135 -16.76350 73.77350 number of atom coordinates read : 2923 total number of charged atoms : 2770 net assigned charge : 8.000016 assigned positive charge : 426.8099 centred at (gu) : 88.22822 88.30399 89.33559 assigned negative charge : -418.8103 centred at (gu) : 88.32099 88.48452 88.85551 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33636 grid for indexing accessible points = 1.400000 m= 21293 mr = 40144 m= 2684 mr = 13296 m= 114 mr = 1153 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.5300000 number of dielectric boundary points 37784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21454 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) : 0.5729829 object centre at (A) : 144.3135 -16.76350 73.77350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9219617E-03 2.9842537E-02 midg,1,midg; midg,igrid,midg 1.3814121E-02 1.0009092E-02 1,midg,midg; igrid,midg,midg 2.2477743E-03 4.5498367E-03 gauss-seidel spectral radius is 0.9983972 estimated iterations to convergence 198 setup time was (sec) 0.8400000 now iterating at: 09:45:03 rms-change max change #iterations 3.601563 176.4701 at 10iterations 1.574766 65.59440 at 20iterations 0.6897200 30.21864 at 30iterations 0.3019612 11.52249 at 40iterations 0.1319309 5.751526 at 50iterations 5.8001176E-02 2.118347 at 60iterations 2.5364146E-02 0.9594296 at 70iterations 1.1069424E-02 0.3745422 at 80iterations 4.8759500E-03 0.1951218 at 90iterations 2.1463542E-03 7.6693535E-02 at 100iterations 9.3862176E-04 3.3950329E-02 at 110iterations 4.1255530E-04 1.4655650E-02 at 120iterations finished qdiffx linear iterations at : 09:45:11 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 4.1255530E-04 1.4655650E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.010000 DelPhi exited at 09:45:11 9.015u 0.205s 0:09.64 95.5% 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 09:45:11 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 = 2923 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: 2.578423 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): 113.2480 175.3790 ymin,ymax (A): -43.69800 10.17100 zmin,zma (A): 45.89500 101.6520 x,y,z range (A): 62.13100 53.86900 55.75700 scale (grids/A): 2.578423 object centre (A): 144.3135 -16.76350 73.77350 number of atom coordinates read : 2923 total number of charged atoms : 2770 net assigned charge : 8.000016 assigned positive charge : 426.8099 centred at (gu) : 87.34212 87.45570 89.00336 assigned negative charge : -418.8103 centred at (gu) : 87.48134 87.72662 88.28324 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 157384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33636 grid for indexing accessible points = 1.400000 m= 69816 mr = 99497 m= 22947 mr = 51101 m= 4188 mr = 16293 m= 343 mr = 2363 m= 10 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 1.360000 number of dielectric boundary points 85289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22156 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) : 1.718949 object centre at (A) : 144.3135 -16.76350 73.77350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3215881E-02 0.4126686 midg,1,midg; midg,igrid,midg 0.1849169 0.1540755 1,midg,midg; igrid,midg,midg 6.9415651E-02 -6.6170404E-03 gauss-seidel spectral radius is 0.9992292 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 09:45:13 rms-change max change #iterations 9.284331 358.9602 at 10iterations 5.520617 151.4306 at 20iterations 3.233592 81.21351 at 30iterations 1.875813 43.97381 at 40iterations 1.083820 24.30913 at 50iterations 0.6237335 14.21886 at 60iterations 0.3580170 8.147614 at 70iterations 0.2053491 4.745360 at 80iterations 0.1172583 2.933141 at 90iterations 6.6909418E-02 1.379155 at 100iterations 3.8242999E-02 0.8626099 at 110iterations 2.1713842E-02 0.4847240 at 120iterations 1.2351795E-02 0.2657051 at 130iterations 7.0244633E-03 0.1512833 at 140iterations 3.9880350E-03 7.9147339E-02 at 150iterations 2.2718422E-03 4.4140816E-02 at 160iterations 1.2876467E-03 2.8284073E-02 at 170iterations 7.3320727E-04 1.4673233E-02 at 180iterations finished qdiffx linear iterations at : 09:45:23 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 7.3320727E-04 1.4673233E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 09:45:24 12.120u 0.185s 0:12.60 97.6% 0+0k 0+0io 0pf+0w