Sun Oct 9 03:04:13 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 Sun Oct 9 2011 at 03:04:13 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4584 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.4454789 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): -2.876000 77.03800 ymin,ymax (A): 0.6680001 67.46799 zmin,zma (A): 167.5620 228.5290 x,y,z range (A): 79.91400 66.80000 60.96698 scale (grids/A): 0.4454789 object centre (A): 37.08100 34.06800 198.0455 number of atom coordinates read : 4584 total number of charged atoms : 4350 net assigned charge : 19.00001 assigned positive charge : 670.5859 centred at (gu) : 86.03329 91.04940 88.66030 assigned negative charge : -651.5907 centred at (gu) : 85.97924 90.99954 88.68542 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5440 nv = 96 ne = 84 npr = 93822 no. pairs analyzed = 93822 no. exposed pairs = 5718 no. arc points = 39388 no. surface atoms = 1957 nbur = 2627 mkacc time = 0.1600000 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 = 1.904000 m= 147 mr = 2632 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3379 ## 688 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7784102E-11 4.9196055E-12 midg,1,midg; midg,igrid,midg 3.6189606E-12 1.9492524E-11 1,midg,midg; igrid,midg,midg 1.3707575E-11 4.6618161E-12 gauss-seidel spectral radius is 0.9742781 estimated iterations to convergence 52 setup time was (sec) 0.5100000 now iterating at: 03:04:14 rms-change max change #iterations 3.3461493E-02 8.369837 at 10iterations 2.6804102E-03 0.4971886 at 20iterations 4.7183881E-04 8.9954376E-02 at 30iterations 9.1192735E-05 1.7112732E-02 at 40iterations 1.7736933E-05 3.3073425E-03 at 50iterations finished qdiffx linear iterations at : 03:04:17 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.7736933E-05 3.3073425E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 03:04:17 3.622u 0.162s 0:04.17 90.6% 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 Sun Oct 9 2011 at 03:04:17 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4584 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.336437 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): -2.876000 77.03800 ymin,ymax (A): 0.6680001 67.46799 zmin,zma (A): 167.5620 228.5290 x,y,z range (A): 79.91400 66.80000 60.96698 scale (grids/A): 1.336437 object centre (A): 37.08100 34.06800 198.0455 number of atom coordinates read : 4584 total number of charged atoms : 4350 net assigned charge : 19.00001 assigned positive charge : 670.5859 centred at (gu) : 78.09811 93.14648 85.97923 assigned negative charge : -651.5907 centred at (gu) : 77.93752 92.99838 86.05629 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39388 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 15196 mr = 41986 m= 780 mr = 9347 m= 7 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 895 time to turn everything in is 0.3600000 number of dielectric boundary points 27680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 660 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 30813 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) : 0.4454789 object centre at (A) : 37.08100 34.06800 198.0455 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2622322E-03 8.1087841E-04 midg,1,midg; midg,igrid,midg 2.4494282E-03 3.6262055E-03 1,midg,midg; igrid,midg,midg 2.1952203E-02 3.2925804E-03 gauss-seidel spectral radius is 0.9973849 estimated iterations to convergence 156 setup time was (sec) 0.6000000 now iterating at: 03:04:18 rms-change max change #iterations 2.561233 128.8446 at 10iterations 0.8926833 36.42998 at 20iterations 0.3145132 12.35702 at 30iterations 0.1109448 4.577512 at 40iterations 3.9136484E-02 1.577220 at 50iterations 1.4062775E-02 0.5067711 at 60iterations 5.2252212E-03 0.2056522 at 70iterations 2.0686982E-03 7.8151703E-02 at 80iterations 9.0941298E-04 3.4473419E-02 at 90iterations 4.4482618E-04 1.4361382E-02 at 100iterations 2.3600730E-04 8.1863403E-03 at 110iterations 1.2974179E-04 3.9196014E-03 at 120iterations finished qdiffx linear iterations at : 03:04:26 total time elapsed so far: 8.360000 # loops : 120 mean,max change (kT/e) : 1.2974179E-04 3.9196014E-03 energy calculations done at 8.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 03:04:26 8.489u 0.243s 0:09.16 95.1% 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 03:04:26 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4584 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.004655 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): -2.876000 77.03800 ymin,ymax (A): 0.6680001 67.46799 zmin,zma (A): 167.5620 228.5290 x,y,z range (A): 79.91400 66.80000 60.96698 scale (grids/A): 2.004655 object centre (A): 37.08100 34.06800 198.0455 number of atom coordinates read : 4584 total number of charged atoms : 4350 net assigned charge : 19.00001 assigned positive charge : 670.5859 centred at (gu) : 72.14668 94.71936 83.96848 assigned negative charge : -651.5907 centred at (gu) : 71.90617 94.49738 84.08414 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39388 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 58408 mr = 104589 m= 11253 mr = 43715 m= 926 mr = 7399 m= 17 mr = 394 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3179 time to turn everything in is 0.8000000 number of dielectric boundary points 62590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 34458 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) : 1.336437 object centre at (A) : 37.08100 34.06800 198.0455 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2247496E-02 1.2602427E-02 midg,1,midg; midg,igrid,midg 5.0342053E-02 6.3298889E-02 1,midg,midg; igrid,midg,midg 0.4977077 4.0165912E-02 gauss-seidel spectral radius is 0.9988996 estimated iterations to convergence 239 setup time was (sec) 1.060000 now iterating at: 03:04:28 rms-change max change #iterations 7.641486 221.9551 at 10iterations 3.997680 111.6417 at 20iterations 2.083977 51.27685 at 30iterations 1.077265 27.14962 at 40iterations 0.5568717 13.61700 at 50iterations 0.2864298 7.860580 at 60iterations 0.1469156 3.832653 at 70iterations 7.5243898E-02 1.795354 at 80iterations 3.8513113E-02 0.8126297 at 90iterations 1.9693773E-02 0.4644508 at 100iterations 1.0061210E-02 0.2340536 at 110iterations 5.1524527E-03 0.1191196 at 120iterations 2.6345029E-03 5.9806824E-02 at 130iterations 1.3567938E-03 3.1114578E-02 at 140iterations 7.0059247E-04 1.5686035E-02 at 150iterations 3.6639950E-04 8.3465576E-03 at 160iterations 1.9436059E-04 4.2457581E-03 at 170iterations 1.0515624E-04 2.3860931E-03 at 180iterations finished qdiffx linear iterations at : 03:04:40 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 1.0515624E-04 2.3860931E-03 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 03:04:40 13.429u 0.245s 0:14.12 96.7% 0+0k 0+0io 0pf+0w