Tue Oct 11 01:06:15 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 Tue Oct 11 2011 at 01:06:15 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 = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6400000 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): -2.416000 53.20900 ymin,ymax (A): 5.672000 58.38900 zmin,zma (A): 7.214000 50.23600 x,y,z range (A): 55.62500 52.71700 43.02200 scale (grids/A): 0.6400000 object centre (A): 25.39650 32.03050 28.72500 number of atom coordinates read : 2590 total number of charged atoms : 2448 net assigned charge : 4.000012 assigned positive charge : 388.2368 centred at (gu) : 89.20583 89.16367 90.31591 assigned negative charge : -384.2373 centred at (gu) : 89.33285 89.13079 90.49889 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7090 nv = 96 ne = 84 npr = 52862 no. pairs analyzed = 52862 no. exposed pairs = 3075 no. arc points = 21352 no. surface atoms = 1050 nbur = 1540 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 4020 m= 0 mr = 41 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.1900000 number of dielectric boundary points 3403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8472 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4779998E-08 -1.6858030E-08 midg,1,midg; midg,igrid,midg 2.3596438E-09 8.0596587E-09 1,midg,midg; igrid,midg,midg 2.4074856E-08 -7.5523463E-09 gauss-seidel spectral radius is 0.9873485 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 01:06:15 rms-change max change #iterations 0.1445796 18.95474 at 10iterations 1.5368601E-02 2.129009 at 20iterations 2.1501340E-03 0.3822479 at 30iterations 4.9739116E-04 0.1044464 at 40iterations 1.4198432E-04 2.9880524E-02 at 50iterations finished qdiffx linear iterations at : 01:06:18 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.4198432E-04 2.9880524E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 01:06:19 3.345u 0.178s 0:03.92 89.5% 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 Tue Oct 11 2011 at 01:06:19 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 = 2590 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: 1.920000 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): -2.416000 53.20900 ymin,ymax (A): 5.672000 58.38900 zmin,zma (A): 7.214000 50.23600 x,y,z range (A): 55.62500 52.71700 43.02200 scale (grids/A): 1.920000 object centre (A): 25.39650 32.03050 28.72500 number of atom coordinates read : 2590 total number of charged atoms : 2448 net assigned charge : 4.000012 assigned positive charge : 388.2368 centred at (gu) : 87.61664 87.49047 90.94698 assigned negative charge : -384.2373 centred at (gu) : 87.99837 87.39233 91.49641 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21352 grid for indexing accessible points = 1.400000 m= 27726 mr = 54089 m= 4376 mr = 20794 m= 244 mr = 2733 m= 6 mr = 95 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 590 time to turn everything in is 0.3700000 number of dielectric boundary points 31420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19258 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) : 0.6400000 object centre at (A) : 25.39650 32.03050 28.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1588621E-02 3.7030678E-03 midg,1,midg; midg,igrid,midg -4.6447236E-03 9.6900733E-03 1,midg,midg; igrid,midg,midg 2.7848925E-02 -2.1161025E-02 gauss-seidel spectral radius is 0.9986498 estimated iterations to convergence 216 setup time was (sec) 0.5900000 now iterating at: 01:06:19 rms-change max change #iterations 4.281868 169.2290 at 10iterations 2.006453 70.24561 at 20iterations 0.9453459 30.61451 at 30iterations 0.4429010 15.74212 at 40iterations 0.2084818 7.575752 at 50iterations 9.8278083E-02 3.003819 at 60iterations 4.6443336E-02 1.434937 at 70iterations 2.1985460E-02 0.6845341 at 80iterations 1.0555966E-02 0.3296928 at 90iterations 5.1309513E-03 0.1677399 at 100iterations 2.5621927E-03 8.9908600E-02 at 110iterations 1.3486597E-03 5.1959991E-02 at 120iterations finished qdiffx linear iterations at : 01:06:27 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.3486597E-03 5.1959991E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 01:06:27 7.875u 0.217s 0:08.53 94.7% 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 Tue Oct 11 2011 at 01:06:27 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 = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.880000 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): -2.416000 53.20900 ymin,ymax (A): 5.672000 58.38900 zmin,zma (A): 7.214000 50.23600 x,y,z range (A): 55.62500 52.71700 43.02200 scale (grids/A): 2.880000 object centre (A): 25.39650 32.03050 28.72500 number of atom coordinates read : 2590 total number of charged atoms : 2448 net assigned charge : 4.000012 assigned positive charge : 388.2368 centred at (gu) : 86.42487 86.23559 91.42032 assigned negative charge : -384.2373 centred at (gu) : 86.99749 86.08844 92.24459 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 177787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21352 grid for indexing accessible points = 1.400000 m= 90733 mr = 131117 m= 32474 mr = 75049 m= 7685 mr = 26246 m= 1060 mr = 5885 m= 61 mr = 681 m= 3 mr = 29 m= 0 mr = 1 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2162 time to turn everything in is 0.9500000 number of dielectric boundary points 70795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19579 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) : 1.920000 object centre at (A) : 25.39650 32.03050 28.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2985782 0.1034892 midg,1,midg; midg,igrid,midg 0.2379545 0.1470194 1,midg,midg; igrid,midg,midg 0.2887996 -0.1670495 gauss-seidel spectral radius is 0.9992567 estimated iterations to convergence 289 setup time was (sec) 1.190000 now iterating at: 01:06:29 rms-change max change #iterations 9.930288 427.9697 at 10iterations 5.732473 123.0047 at 20iterations 3.308104 58.89057 at 30iterations 1.902728 38.31042 at 40iterations 1.098317 21.66574 at 50iterations 0.6294993 11.15184 at 60iterations 0.3624181 6.918850 at 70iterations 0.2081052 3.807819 at 80iterations 0.1194838 2.253410 at 90iterations 6.8728939E-02 1.203197 at 100iterations 3.9523959E-02 0.7774353 at 110iterations 2.2780739E-02 0.4572906 at 120iterations 1.3192678E-02 0.2406864 at 130iterations 7.7307210E-03 0.1511497 at 140iterations 4.6196221E-03 9.2220306E-02 at 150iterations 2.8312034E-03 6.1893463E-02 at 160iterations 1.8079953E-03 4.0603638E-02 at 170iterations 1.2308558E-03 2.8388977E-02 at 180iterations finished qdiffx linear iterations at : 01:06:40 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 1.2308558E-03 2.8388977E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 01:06:40 12.380u 0.195s 0:12.85 97.8% 0+0k 0+0io 0pf+0w