Sat Oct 8 20:52:05 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+sph2.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 = amb2.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 20:52:05 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 = 2579 !!! WARNING: GLM 89 has a net charge of -0.0940 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: HIR 116 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6214433 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): -32.29200 17.50500 ymin,ymax (A): -23.63000 22.27900 zmin,zma (A): -12.62000 44.66600 x,y,z range (A): 49.79700 45.90900 57.28600 scale (grids/A): 0.6214433 object centre (A): -7.393500 -0.6754999 16.02300 number of atom coordinates read : 2579 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 88.72050 89.36340 89.77329 assigned negative charge : -389.5226 centred at (gu) : 88.61669 89.40332 89.68566 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 54348 no. pairs analyzed = 54348 no. exposed pairs = 2934 no. arc points = 20959 no. surface atoms = 990 nbur = 1589 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3610 m= 0 mr = 26 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 93 time to turn everything in is 0.3000000 number of dielectric boundary points 3108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2157 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3134271E-09 8.5862268E-09 midg,1,midg; midg,igrid,midg 6.6224422E-09 2.0805294E-10 1,midg,midg; igrid,midg,midg -5.7870588E-09 7.6510762E-09 gauss-seidel spectral radius is 0.9865816 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 20:52:06 rms-change max change #iterations 0.1260762 20.46666 at 10iterations 1.1659876E-02 1.676666 at 20iterations 1.0800031E-03 0.1629028 at 30iterations 9.9080258E-05 1.6578674E-02 at 40iterations 9.3592516E-06 1.3484955E-03 at 50iterations finished qdiffx linear iterations at : 20:52:10 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 9.3592516E-06 1.3484955E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 20:52:10 4.784u 0.388s 0:05.43 95.0% 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 Sat Oct 8 2011 at 20:52:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: GLM 89 has a net charge of -0.0940 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: HIR 116 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.864330 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): -32.29200 17.50500 ymin,ymax (A): -23.63000 22.27900 zmin,zma (A): -12.62000 44.66600 x,y,z range (A): 49.79700 45.90900 57.28600 scale (grids/A): 1.864330 object centre (A): -7.393500 -0.6754999 16.02300 number of atom coordinates read : 2579 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 86.16113 88.08971 89.31914 assigned negative charge : -389.5226 centred at (gu) : 85.84967 88.20969 89.05675 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20959 grid for indexing accessible points = 1.400000 m= 23507 mr = 49023 m= 3109 mr = 17123 m= 136 mr = 1855 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3712 time to turn everything in is 0.6100000 number of dielectric boundary points 28604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19214 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) : 0.6214433 object centre at (A) : -7.393500 -0.6754999 16.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2809992E-02 1.8854022E-02 midg,1,midg; midg,igrid,midg 1.1337785E-02 3.7264568E-03 1,midg,midg; igrid,midg,midg -9.7440667E-03 3.3250060E-02 gauss-seidel spectral radius is 0.9985690 estimated iterations to convergence 210 setup time was (sec) 0.9000000 now iterating at: 20:52:12 rms-change max change #iterations 4.051765 170.6165 at 10iterations 1.869805 69.39375 at 20iterations 0.8589777 27.55021 at 30iterations 0.3949162 12.95354 at 40iterations 0.1824228 6.093388 at 50iterations 8.3658382E-02 2.968365 at 60iterations 3.8711082E-02 1.344065 at 70iterations 1.7725751E-02 0.5310588 at 80iterations 8.1886295E-03 0.2690430 at 90iterations 3.7664531E-03 0.1209793 at 100iterations 1.7319977E-03 6.2482834E-02 at 110iterations 7.9764629E-04 2.6894331E-02 at 120iterations finished qdiffx linear iterations at : 20:52:21 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 7.9764629E-04 2.6894331E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 20:52:22 10.869u 0.438s 0:11.60 97.3% 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 Sat Oct 8 2011 at 20:52:22 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 = 2579 !!! WARNING: GLM 89 has a net charge of -0.0940 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: HIR 116 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.796495 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): -32.29200 17.50500 ymin,ymax (A): -23.63000 22.27900 zmin,zma (A): -12.62000 44.66600 x,y,z range (A): 49.79700 45.90900 57.28600 scale (grids/A): 2.796495 object centre (A): -7.393500 -0.6754999 16.02300 number of atom coordinates read : 2579 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 84.24165 87.13435 88.97855 assigned negative charge : -389.5226 centred at (gu) : 83.77444 87.31451 88.58508 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20959 grid for indexing accessible points = 1.400000 m= 78491 mr = 118549 m= 25420 mr = 64436 m= 5309 mr = 20180 m= 587 mr = 3870 m= 25 mr = 368 m= 0 mr = 11 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 12318 time to turn everything in is 1.440000 number of dielectric boundary points 64547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19590 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) : 1.864330 object centre at (A) : -7.393500 -0.6754999 16.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1044514 0.1868342 midg,1,midg; midg,igrid,midg 0.1359550 1.8986542E-02 1,midg,midg; igrid,midg,midg -7.2738931E-02 0.4498626 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.770000 now iterating at: 20:52:24 rms-change max change #iterations 9.521841 309.5499 at 10iterations 5.455055 122.5290 at 20iterations 3.117993 73.94046 at 30iterations 1.776276 34.54559 at 40iterations 1.012190 18.85759 at 50iterations 0.5750574 13.15252 at 60iterations 0.3279008 6.150189 at 70iterations 0.1860745 3.538576 at 80iterations 0.1058968 2.202436 at 90iterations 6.0204022E-02 1.133015 at 100iterations 3.4160957E-02 0.6841984 at 110iterations 1.9472618E-02 0.3638687 at 120iterations 1.1066407E-02 0.2105341 at 130iterations 6.2831077E-03 0.1156406 at 140iterations 3.5706752E-03 6.6421509E-02 at 150iterations 2.0303114E-03 3.8348198E-02 at 160iterations 1.1564221E-03 2.1181583E-02 at 170iterations 6.5595272E-04 1.3550282E-02 at 180iterations finished qdiffx linear iterations at : 20:52:41 total time elapsed so far: 18.60000 # loops : 180 mean,max change (kT/e) : 6.5595272E-04 1.3550282E-02 energy calculations done at 18.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.76000 DelPhi exited at 20:52:41 18.765u 0.468s 0:19.49 98.6% 0+0k 0+0io 0pf+0w