Tue Oct 11 06:01:10 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 06:01:10 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 0.7112318 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): 25.86000 72.64100 ymin,ymax (A): -18.63200 31.42200 zmin,zma (A): 4.252000 46.54500 x,y,z range (A): 46.78100 50.05400 42.29300 scale (grids/A): 0.7112318 object centre (A): 49.25050 6.395000 25.39850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 89.15079 90.18128 90.21052 assigned negative charge : -317.2741 centred at (gu) : 89.28901 90.12582 90.29180 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7245 nv = 96 ne = 84 npr = 42543 no. pairs analyzed = 42543 no. exposed pairs = 2598 no. arc points = 17667 no. surface atoms = 885 nbur = 1433 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 4208 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1614 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7999 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9344803E-08 1.4980978E-08 midg,1,midg; midg,igrid,midg 2.7940903E-08 9.2655220E-08 1,midg,midg; igrid,midg,midg 1.5794366E-07 -1.4111556E-08 gauss-seidel spectral radius is 0.9896970 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 06:01:11 rms-change max change #iterations 0.2046484 30.25924 at 10iterations 2.5599992E-02 3.472927 at 20iterations 3.3817361E-03 0.4841561 at 30iterations 5.4497510E-04 7.3225021E-02 at 40iterations 1.3306808E-04 1.6750336E-02 at 50iterations finished qdiffx linear iterations at : 06:01:15 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 1.3306808E-04 1.6750336E-02 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 06:01:16 4.673u 0.372s 0:05.52 91.3% 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 06:01:16 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 2.133696 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): 25.86000 72.64100 ymin,ymax (A): -18.63200 31.42200 zmin,zma (A): 4.252000 46.54500 x,y,z range (A): 46.78100 50.05400 42.29300 scale (grids/A): 2.133696 object centre (A): 49.25050 6.395000 25.39850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 87.45235 90.54386 90.63148 assigned negative charge : -317.2741 centred at (gu) : 87.86694 90.37768 90.87534 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17667 grid for indexing accessible points = 1.400000 m= 31573 mr = 54972 m= 6285 mr = 24159 m= 571 mr = 4246 m= 15 mr = 274 m= 0 mr = 3 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 31707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15828 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) : 0.7112318 object centre at (A) : 49.25050 6.395000 25.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2888638E-02 3.2372698E-02 midg,1,midg; midg,igrid,midg 4.8352197E-02 2.8721508E-02 1,midg,midg; igrid,midg,midg 4.5367014E-02 -5.5074088E-02 gauss-seidel spectral radius is 0.9988453 estimated iterations to convergence 233 setup time was (sec) 0.9600000 now iterating at: 06:01:17 rms-change max change #iterations 4.659985 213.1844 at 10iterations 2.318126 78.21187 at 20iterations 1.153200 36.40614 at 30iterations 0.5753793 16.95192 at 40iterations 0.2878483 8.270989 at 50iterations 0.1428424 4.051289 at 60iterations 7.1274593E-02 2.024487 at 70iterations 3.5685211E-02 1.065995 at 80iterations 1.7832771E-02 0.5468760 at 90iterations 8.9616124E-03 0.2730076 at 100iterations 4.5205802E-03 0.1333599 at 110iterations 2.3266375E-03 7.6562881E-02 at 120iterations finished qdiffx linear iterations at : 06:01:27 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 2.3266375E-03 7.6562881E-02 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 06:01:27 10.684u 0.436s 0:11.66 95.2% 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 Tue Oct 11 2011 at 06:01:28 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 3.200543 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): 25.86000 72.64100 ymin,ymax (A): -18.63200 31.42200 zmin,zma (A): 4.252000 46.54500 x,y,z range (A): 46.78100 50.05400 42.29300 scale (grids/A): 3.200543 object centre (A): 49.25050 6.395000 25.39850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 86.17848 90.81583 90.94720 assigned negative charge : -317.2741 centred at (gu) : 86.80035 90.56644 91.31299 start vw surface at 0.1000000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 177060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17667 grid for indexing accessible points = 1.400000 m= 97741 mr = 131983 m= 40717 mr = 81797 m= 11882 mr = 33581 m= 2430 mr = 9306 m= 320 mr = 1760 m= 20 mr = 224 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 71512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 15952 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) : 2.133696 object centre at (A) : 49.25050 6.395000 25.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1219107 0.2467878 midg,1,midg; midg,igrid,midg 0.4107665 0.1435469 1,midg,midg; igrid,midg,midg 0.4520975 -0.6752408 gauss-seidel spectral radius is 0.9992993 estimated iterations to convergence 298 setup time was (sec) 2.420000 now iterating at: 06:01:30 rms-change max change #iterations 10.36371 346.1987 at 10iterations 6.140599 136.8229 at 20iterations 3.636695 88.17111 at 30iterations 2.149055 42.41411 at 40iterations 1.266430 24.83291 at 50iterations 0.7454809 13.10536 at 60iterations 0.4386707 8.036426 at 70iterations 0.2573993 4.566527 at 80iterations 0.1515098 2.567632 at 90iterations 8.8901527E-02 1.488190 at 100iterations 5.2157223E-02 0.9314132 at 110iterations 3.0700386E-02 0.5291979 at 120iterations 1.8167151E-02 0.2973633 at 130iterations 1.0869134E-02 0.1953659 at 140iterations 6.6229450E-03 0.1255493 at 150iterations 4.1446276E-03 8.4106445E-02 at 160iterations 2.7146921E-03 5.6430817E-02 at 170iterations 1.8815942E-03 3.8116455E-02 at 180iterations finished qdiffx linear iterations at : 06:01:47 total time elapsed so far: 19.47000 # loops : 180 mean,max change (kT/e) : 1.8815942E-03 3.8116455E-02 energy calculations done at 19.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.64000 DelPhi exited at 06:01:48 19.642u 0.459s 0:20.39 98.5% 0+0k 0+0io 0pf+0w