Mon Oct 10 14:06:46 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 Mon Oct 10 2011 at 14:06:46 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 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: 0.5966647 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 0.5966647 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 463.8612 centred at (gu) : 90.14091 89.29990 91.05962 assigned negative charge : -461.8622 centred at (gu) : 90.12787 89.25777 91.08714 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7254 nv = 96 ne = 84 npr = 64039 no. pairs analyzed = 64039 no. exposed pairs = 3626 no. arc points = 25609 no. surface atoms = 1204 nbur = 1903 mkacc time = 0.1700000 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= 326 mr = 4056 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3900000 number of dielectric boundary points 3498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2622 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4669601E-09 -3.7942646E-10 midg,1,midg; midg,igrid,midg -1.0231840E-09 2.0726045E-09 1,midg,midg; igrid,midg,midg 2.7400243E-10 1.3431855E-09 gauss-seidel spectral radius is 0.9855023 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 14:06:47 rms-change max change #iterations 0.1159304 18.93585 at 10iterations 1.1640018E-02 1.803032 at 20iterations 2.5294160E-03 0.5415955 at 30iterations 8.3949370E-04 0.1876755 at 40iterations 2.9131578E-04 6.5368652E-02 at 50iterations finished qdiffx linear iterations at : 14:06:51 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 2.9131578E-04 6.5368652E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:06:51 4.243u 0.247s 0:04.89 91.6% 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 Mon Oct 10 2011 at 14:06:51 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 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: 1.789994 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 1.789994 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 463.8612 centred at (gu) : 90.42168 87.89928 93.17827 assigned negative charge : -461.8622 centred at (gu) : 90.38330 87.77287 93.26109 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25609 grid for indexing accessible points = 1.400000 m= 27053 mr = 56957 m= 3306 mr = 19649 m= 136 mr = 1895 m= 0 mr = 34 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 433 time to turn everything in is 0.6900000 number of dielectric boundary points 32163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 23081 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) : 0.5966647 object centre at (A) : 31.82850 2.526500 17.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7774983E-03 -1.7787782E-02 midg,1,midg; midg,igrid,midg -2.6490211E-03 7.6869540E-03 1,midg,midg; igrid,midg,midg 2.7709544E-02 1.2247956E-02 gauss-seidel spectral radius is 0.9985068 estimated iterations to convergence 205 setup time was (sec) 1.010000 now iterating at: 14:06:53 rms-change max change #iterations 4.131763 179.6653 at 10iterations 1.857556 62.91159 at 20iterations 0.8435383 30.91223 at 30iterations 0.3817294 14.15694 at 40iterations 0.1741741 5.731848 at 50iterations 7.9103902E-02 2.642939 at 60iterations 3.6232900E-02 1.219320 at 70iterations 1.6971573E-02 0.5407028 at 80iterations 8.1096012E-03 0.3019371 at 90iterations 4.1070823E-03 0.1635056 at 100iterations 2.2486257E-03 9.1590881E-02 at 110iterations 1.3272857E-03 5.7811737E-02 at 120iterations finished qdiffx linear iterations at : 14:07:01 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 1.3272857E-03 5.7811737E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 14:07:01 9.549u 0.230s 0:10.12 96.5% 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 14:07:02 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 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: 2.684991 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 2.684991 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 463.8612 centred at (gu) : 90.63255 86.84857 94.76714 assigned negative charge : -461.8622 centred at (gu) : 90.57491 86.65921 94.89145 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 186521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25609 grid for indexing accessible points = 1.400000 m= 91432 mr = 138627 m= 28437 mr = 74643 m= 5578 mr = 22399 m= 565 mr = 4074 m= 27 mr = 338 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 1611 time to turn everything in is 1.610000 number of dielectric boundary points 72470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 23710 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) : 1.789994 object centre at (A) : 31.82850 2.526500 17.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4350375E-02 -0.1455555 midg,1,midg; midg,igrid,midg -4.7616184E-02 0.1022792 1,midg,midg; igrid,midg,midg 0.5337881 0.1962230 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 1.940000 now iterating at: 14:07:04 rms-change max change #iterations 9.938369 341.1389 at 10iterations 5.732219 140.8000 at 20iterations 3.297497 66.07343 at 30iterations 1.891264 39.08739 at 40iterations 1.079448 19.67625 at 50iterations 0.6172254 12.02895 at 60iterations 0.3522769 6.655018 at 70iterations 0.2009021 3.694678 at 80iterations 0.1144930 2.082264 at 90iterations 6.5136589E-02 1.224236 at 100iterations 3.7179220E-02 0.6686230 at 110iterations 2.1346707E-02 0.3874321 at 120iterations 1.2292258E-02 0.2198696 at 130iterations 7.1641561E-03 0.1388016 at 140iterations 4.2787623E-03 8.4869385E-02 at 150iterations 2.6474297E-03 5.5541992E-02 at 160iterations 1.7139473E-03 3.9897919E-02 at 170iterations 1.1739273E-03 2.7780533E-02 at 180iterations finished qdiffx linear iterations at : 14:07:17 total time elapsed so far: 15.03000 # loops : 180 mean,max change (kT/e) : 1.1739273E-03 2.7780533E-02 energy calculations done at 15.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.21000 DelPhi exited at 14:07:18 15.216u 0.291s 0:16.06 96.5% 0+0k 0+0io 0pf+0w