Sat Oct 8 13:30:52 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 13:30:52 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6384848 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): -12.10400 43.65300 ymin,ymax (A): -22.28500 22.21800 zmin,zma (A): -8.505000 47.00200 x,y,z range (A): 55.75700 44.50300 55.50700 scale (grids/A): 0.6384848 object centre (A): 15.77450 -3.3499718E-02 19.24850 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -0.9999939 assigned positive charge : 451.2556 centred at (gu) : 88.80750 89.64149 92.25198 assigned negative charge : -452.2563 centred at (gu) : 88.74557 89.54813 92.15710 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8279 nv = 96 ne = 84 npr = 62968 no. pairs analyzed = 62968 no. exposed pairs = 3461 no. arc points = 23696 no. surface atoms = 1182 nbur = 1836 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4921 m= 2 mr = 51 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 3780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2260 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5959133E-09 1.7586640E-08 midg,1,midg; midg,igrid,midg -1.4855530E-08 9.6524184E-09 1,midg,midg; igrid,midg,midg -1.2456191E-08 4.9569220E-09 gauss-seidel spectral radius is 0.9873224 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 13:30:53 rms-change max change #iterations 0.1592043 23.81206 at 10iterations 1.6016718E-02 2.023500 at 20iterations 1.7510762E-03 0.2716599 at 30iterations 2.7048800E-04 3.8909912E-02 at 40iterations 5.7800760E-05 9.6435547E-03 at 50iterations finished qdiffx linear iterations at : 13:30:57 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 5.7800760E-05 9.6435547E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 13:30:57 4.232u 0.250s 0:04.76 94.1% 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 Sat Oct 8 2011 at 13:30:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.915455 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): -12.10400 43.65300 ymin,ymax (A): -22.28500 22.21800 zmin,zma (A): -8.505000 47.00200 x,y,z range (A): 55.75700 44.50300 55.50700 scale (grids/A): 1.915455 object centre (A): 15.77450 -3.3499718E-02 19.24850 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -0.9999939 assigned positive charge : 451.2556 centred at (gu) : 86.42191 88.92386 96.75540 assigned negative charge : -452.2563 centred at (gu) : 86.23624 88.64402 96.47086 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23696 grid for indexing accessible points = 1.400000 m= 34027 mr = 65460 m= 5498 mr = 26066 m= 307 mr = 3467 m= 3 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 34676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 22619 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) : 0.6384848 object centre at (A) : 15.77450 -3.3499718E-02 19.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3255372E-02 2.4997817E-02 midg,1,midg; midg,igrid,midg -2.8442719E-03 1.5496298E-02 1,midg,midg; igrid,midg,midg -6.5802976E-02 1.3602279E-02 gauss-seidel spectral radius is 0.9986821 estimated iterations to convergence 218 setup time was (sec) 0.9800000 now iterating at: 13:30:58 rms-change max change #iterations 4.701619 198.2048 at 10iterations 2.244787 63.88531 at 20iterations 1.065347 32.75692 at 30iterations 0.5068141 14.39323 at 40iterations 0.2400874 6.865892 at 50iterations 0.1148332 3.261962 at 60iterations 5.4700010E-02 1.633366 at 70iterations 2.5874930E-02 0.7414913 at 80iterations 1.2407674E-02 0.3693962 at 90iterations 5.9213634E-03 0.1801834 at 100iterations 2.8389983E-03 9.4146729E-02 at 110iterations 1.3667975E-03 3.6717415E-02 at 120iterations finished qdiffx linear iterations at : 13:31:07 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 1.3667975E-03 3.6717415E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 13:31:08 9.838u 0.279s 0:10.40 97.1% 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 Sat Oct 8 2011 at 13:31:08 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: NAP 318 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.873182 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): -12.10400 43.65300 ymin,ymax (A): -22.28500 22.21800 zmin,zma (A): -8.505000 47.00200 x,y,z range (A): 55.75700 44.50300 55.50700 scale (grids/A): 2.873182 object centre (A): 15.77450 -3.3499718E-02 19.24850 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -0.9999939 assigned positive charge : 451.2556 centred at (gu) : 84.63283 88.38566 100.1330 assigned negative charge : -452.2563 centred at (gu) : 84.35442 87.96602 99.70638 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 207955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23696 grid for indexing accessible points = 1.400000 m= 109728 mr = 157666 m= 40928 mr = 92012 m= 9835 mr = 33526 m= 1399 mr = 7560 m= 58 mr = 880 m= 0 mr = 16 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 78243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 22968 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) : 1.915455 object centre at (A) : 15.77450 -3.3499718E-02 19.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1060036 0.3083158 midg,1,midg; midg,igrid,midg 1.4895471E-02 0.1875977 1,midg,midg; igrid,midg,midg -0.9254429 0.2307135 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.060000 now iterating at: 13:31:10 rms-change max change #iterations 10.97361 422.2583 at 10iterations 6.468257 171.4473 at 20iterations 3.790200 80.50589 at 30iterations 2.217560 44.84830 at 40iterations 1.288495 23.52479 at 50iterations 0.7511520 13.53509 at 60iterations 0.4363394 7.811554 at 70iterations 0.2534722 4.529738 at 80iterations 0.1470902 2.399536 at 90iterations 8.5255153E-02 1.562696 at 100iterations 4.9504507E-02 0.8011074 at 110iterations 2.8664635E-02 0.4649544 at 120iterations 1.6618799E-02 0.2621765 at 130iterations 9.6544269E-03 0.1610026 at 140iterations 5.5977032E-03 9.7784519E-02 at 150iterations 3.2581084E-03 5.1424026E-02 at 160iterations 1.9060147E-03 3.2812119E-02 at 170iterations 1.1232581E-03 1.8062592E-02 at 180iterations finished qdiffx linear iterations at : 13:31:24 total time elapsed so far: 15.75000 # loops : 180 mean,max change (kT/e) : 1.1232581E-03 1.8062592E-02 energy calculations done at 15.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.93000 DelPhi exited at 13:31:24 15.932u 0.312s 0:16.56 98.0% 0+0k 0+0io 0pf+0w