Sun Feb 12 05:09:41 PST 2012 #!/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_thin.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 Feb 12 2012 at 05:09:41 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 = 3188 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: 0.6010062 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 0.6010062 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3188 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 89.04030 89.55356 88.55474 assigned negative charge : -425.1732 centred at (gu) : 88.90827 89.71317 88.59105 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7746 nv = 96 ne = 84 npr = 69256 no. pairs analyzed = 69256 no. exposed pairs = 4532 no. arc points = 31933 no. surface atoms = 1523 nbur = 1665 mkacc time = 0.1200000 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 = 1.456000 m= 408 mr = 3513 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3048 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9182422E-09 -1.0163340E-10 midg,1,midg; midg,igrid,midg 8.6139700E-09 -4.8188387E-09 1,midg,midg; igrid,midg,midg -5.2385909E-09 5.3712039E-09 gauss-seidel spectral radius is 0.9857424 estimated iterations to convergence 69 setup time was (sec) 0.4400000 now iterating at: 05:09:42 rms-change max change #iterations 0.1106652 18.44722 at 10iterations 1.0785470E-02 1.539261 at 20iterations 2.6322508E-03 0.4462662 at 30iterations 1.1471719E-03 0.2013359 at 40iterations 5.2302721E-04 9.1735840E-02 at 50iterations finished qdiffx linear iterations at : 05:09:47 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 5.2302721E-04 9.1735840E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 05:09:48 3.643u 0.206s 0:07.19 53.4% 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 Feb 12 2012 at 05:09:48 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 = 3188 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: 1.803018 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 1.803018 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3188 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 87.11962 88.65971 85.66330 assigned negative charge : -425.1732 centred at (gu) : 86.72475 89.13952 85.77279 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31933 grid for indexing accessible points = 1.400000 m= 26605 mr = 52273 m= 3846 mr = 16925 m= 185 mr = 1933 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 42809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 23217 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) : 0.6010062 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5995180E-03 1.1014435E-02 midg,1,midg; midg,igrid,midg -1.0720567E-03 1.2826086E-03 1,midg,midg; igrid,midg,midg -1.4454785E-02 5.1012762E-02 gauss-seidel spectral radius is 0.9985706 estimated iterations to convergence 210 setup time was (sec) 0.6500000 now iterating at: 05:09:49 rms-change max change #iterations 4.024789 185.4473 at 10iterations 1.832530 72.88063 at 20iterations 0.8415143 32.01710 at 30iterations 0.3858549 12.08302 at 40iterations 0.1771914 5.986075 at 50iterations 8.1655622E-02 2.814670 at 60iterations 3.7813660E-02 1.290745 at 70iterations 1.7840777E-02 0.5970535 at 80iterations 8.8234087E-03 0.2732239 at 90iterations 4.8045213E-03 0.1939888 at 100iterations 2.9185987E-03 0.1174431 at 110iterations 1.9991794E-03 7.1186066E-02 at 120iterations finished qdiffx linear iterations at : 05:10:03 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 1.9991794E-03 7.1186066E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 05:10:04 8.438u 0.233s 0:16.01 54.0% 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 Feb 12 2012 at 05:10:04 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 = 3188 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: 2.704528 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 2.704528 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3188 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 85.67937 87.98929 83.49477 assigned negative charge : -425.1732 centred at (gu) : 85.08704 88.70920 83.65896 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 192973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31933 grid for indexing accessible points = 1.400000 m= 86836 mr = 129259 m= 29364 mr = 65061 m= 6448 mr = 21039 m= 727 mr = 4158 m= 33 mr = 323 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 96539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 23758 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) : 1.803018 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1052236 0.1164142 midg,1,midg; midg,igrid,midg -0.1207847 -2.9709639E-02 1,midg,midg; igrid,midg,midg -0.5668572 0.6997737 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 1.360000 now iterating at: 05:10:06 rms-change max change #iterations 10.03073 311.6835 at 10iterations 6.093968 162.0365 at 20iterations 3.659506 85.90915 at 30iterations 2.176742 59.16745 at 40iterations 1.289831 27.22946 at 50iterations 0.7598614 14.10917 at 60iterations 0.4465918 8.679993 at 70iterations 0.2615719 5.013574 at 80iterations 0.1528679 3.002182 at 90iterations 8.9280285E-02 1.712292 at 100iterations 5.2159291E-02 0.9547338 at 110iterations 3.0476375E-02 0.7029305 at 120iterations 1.7887715E-02 0.3631132 at 130iterations 1.0581013E-02 0.2051008 at 140iterations 6.3866680E-03 0.1320953 at 150iterations 3.9970600E-03 8.5586548E-02 at 160iterations 2.6421216E-03 5.7823181E-02 at 170iterations 1.8792214E-03 3.9196014E-02 at 180iterations finished qdiffx linear iterations at : 05:10:32 total time elapsed so far: 14.21000 # loops : 180 mean,max change (kT/e) : 1.8792214E-03 3.9196014E-02 energy calculations done at 14.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.35000 DelPhi exited at 05:10:32 14.356u 0.274s 0:27.98 52.2% 0+0k 0+0io 0pf+0w