Mon Oct 10 17:03:25 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 Mon Oct 10 2011 at 17:03:25 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 = 2698 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: 0.5954871 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 0.5954871 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.000017 assigned positive charge : 395.9126 centred at (gu) : 90.10321 88.94218 90.14370 assigned negative charge : -386.9133 centred at (gu) : 90.05016 88.91851 90.25134 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6397 nv = 96 ne = 84 npr = 53842 no. pairs analyzed = 53842 no. exposed pairs = 3455 no. arc points = 24461 no. surface atoms = 1159 nbur = 1539 mkacc time = 0.1400000 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= 283 mr = 3330 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2482 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4791301E-09 -1.1364248E-10 midg,1,midg; midg,igrid,midg 3.2628324E-09 3.2284886E-09 1,midg,midg; igrid,midg,midg 1.6164363E-09 5.1198543E-09 gauss-seidel spectral radius is 0.9854217 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 17:03:26 rms-change max change #iterations 0.1068373 18.04321 at 10iterations 8.8999327E-03 1.394446 at 20iterations 7.2301383E-04 0.1088753 at 30iterations 6.2052241E-05 8.7547302E-03 at 40iterations 5.6086997E-06 1.0375977E-03 at 50iterations finished qdiffx linear iterations at : 17:03:30 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 5.6086997E-06 1.0375977E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 17:03:32 4.447u 0.403s 0:06.67 72.5% 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 Mon Oct 10 2011 at 17:03:32 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 = 2698 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: 1.786461 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 1.786461 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.000017 assigned positive charge : 395.9126 centred at (gu) : 90.30917 86.82564 90.43031 assigned negative charge : -386.9133 centred at (gu) : 90.15019 86.75510 90.75380 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70030 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24461 grid for indexing accessible points = 1.400000 m= 22656 mr = 47368 m= 2899 mr = 15867 m= 126 mr = 1485 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1286 time to turn everything in is 0.5800000 number of dielectric boundary points 30959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19986 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) : 0.5954871 object centre at (A) : 3.903500 3.053500 22.40400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0333422E-02 1.2806866E-02 midg,1,midg; midg,igrid,midg 1.7245229E-02 2.0233286E-04 1,midg,midg; igrid,midg,midg 5.5278698E-03 7.4447361E-03 gauss-seidel spectral radius is 0.9984655 estimated iterations to convergence 202 setup time was (sec) 0.8700000 now iterating at: 17:03:34 rms-change max change #iterations 3.694583 177.4931 at 10iterations 1.641866 63.77262 at 20iterations 0.7340168 25.77810 at 30iterations 0.3284985 11.44443 at 40iterations 0.1464199 5.094935 at 50iterations 6.5501906E-02 2.218578 at 60iterations 2.9168770E-02 0.9477844 at 70iterations 1.3045459E-02 0.4385147 at 80iterations 5.8423108E-03 0.1999149 at 90iterations 2.6170146E-03 8.7629795E-02 at 100iterations 1.1708890E-03 3.9862633E-02 at 110iterations 5.2392745E-04 1.7426014E-02 at 120iterations finished qdiffx linear iterations at : 17:03:44 total time elapsed so far: 11.26000 # loops : 120 mean,max change (kT/e) : 5.2392745E-04 1.7426014E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 17:03:45 11.443u 0.464s 0:12.45 95.5% 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 Mon Oct 10 2011 at 17:03:45 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 = 2698 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: 2.679692 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 2.679692 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.000017 assigned positive charge : 395.9126 centred at (gu) : 90.46369 85.23846 90.64529 assigned negative charge : -386.9133 centred at (gu) : 90.22519 85.13254 91.13065 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24461 grid for indexing accessible points = 1.400000 m= 75769 mr = 115540 m= 24148 mr = 60380 m= 4844 mr = 18372 m= 529 mr = 3260 m= 27 mr = 286 m= 0 mr = 8 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 4307 time to turn everything in is 1.440000 number of dielectric boundary points 69924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 20485 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) : 1.786461 object centre at (A) : 3.903500 3.053500 22.40400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6074731 0.1638369 midg,1,midg; midg,igrid,midg 0.3186875 3.9263256E-02 1,midg,midg; igrid,midg,midg 8.1447341E-02 5.9953969E-02 gauss-seidel spectral radius is 0.9992165 estimated iterations to convergence 282 setup time was (sec) 1.770000 now iterating at: 17:03:47 rms-change max change #iterations 9.035874 410.0370 at 10iterations 5.202722 113.2755 at 20iterations 2.974228 78.19432 at 30iterations 1.695285 37.74055 at 40iterations 0.9615577 23.64499 at 50iterations 0.5459739 12.11074 at 60iterations 0.3097658 6.134422 at 70iterations 0.1751545 3.667754 at 80iterations 9.8906785E-02 2.185501 at 90iterations 5.5943154E-02 1.227592 at 100iterations 3.1715482E-02 0.7184422 at 110iterations 1.7954946E-02 0.3442963 at 120iterations 1.0105483E-02 0.1863956 at 130iterations 5.7122498E-03 0.1134033 at 140iterations 3.2423502E-03 6.9585562E-02 at 150iterations 1.8294473E-03 3.4541130E-02 at 160iterations 1.0369736E-03 2.1604538E-02 at 170iterations 5.8826053E-04 1.1507988E-02 at 180iterations finished qdiffx linear iterations at : 17:04:03 total time elapsed so far: 17.34000 # loops : 180 mean,max change (kT/e) : 5.8826053E-04 1.1507988E-02 energy calculations done at 17.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.50000 DelPhi exited at 17:04:04 17.504u 0.493s 0:18.61 96.6% 0+0k 0+0io 0pf+0w