Mon Oct 10 17:03:21 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 17:03:21 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 = 4055 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: 0.5492895 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): -21.57800 40.68200 ymin,ymax (A): -28.22500 22.53300 zmin,zma (A): 11.66500 76.47600 x,y,z range (A): 62.26000 50.75800 64.81100 scale (grids/A): 0.5492895 object centre (A): 9.551999 -2.846001 44.07050 number of atom coordinates read : 4055 total number of charged atoms : 3911 net assigned charge : 7.500031 assigned positive charge : 627.1783 centred at (gu) : 90.80708 90.18761 89.07236 assigned negative charge : -619.6826 centred at (gu) : 90.69060 90.09485 88.93140 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 78128 no. pairs analyzed = 78128 no. exposed pairs = 5904 no. arc points = 40757 no. surface atoms = 1953 nbur = 2102 mkacc time = 0.1300000 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 = 1.540000 m= 374 mr = 3662 m= 0 mr = 17 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4085 ## 497 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 10445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2284929E-09 1.5796763E-09 midg,1,midg; midg,igrid,midg -4.2539045E-10 1.5651537E-09 1,midg,midg; igrid,midg,midg -5.6966454E-10 2.1209026E-09 gauss-seidel spectral radius is 0.9830061 estimated iterations to convergence 63 setup time was (sec) 0.4700000 now iterating at: 17:03:22 rms-change max change #iterations 8.9188553E-02 15.85541 at 10iterations 6.1581098E-03 1.009598 at 20iterations 4.8633301E-04 7.5025558E-02 at 30iterations 7.1573340E-05 8.5811615E-03 at 40iterations 1.7219807E-05 1.5435219E-03 at 50iterations finished qdiffx linear iterations at : 17:03:25 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.7219807E-05 1.5435219E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 17:03:25 3.492u 0.183s 0:03.98 92.2% 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 17:03:25 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 = 4055 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: 1.647869 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): -21.57800 40.68200 ymin,ymax (A): -28.22500 22.53300 zmin,zma (A): 11.66500 76.47600 x,y,z range (A): 62.26000 50.75800 64.81100 scale (grids/A): 1.647869 object centre (A): 9.551999 -2.846001 44.07050 number of atom coordinates read : 4055 total number of charged atoms : 3911 net assigned charge : 7.500031 assigned positive charge : 627.1783 centred at (gu) : 92.41989 90.56120 87.21555 assigned negative charge : -619.6826 centred at (gu) : 92.07148 90.28413 86.79364 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 86575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40757 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 28005 mr = 55051 m= 3370 mr = 18020 m= 110 mr = 1396 m= 4 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 43583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 420 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 30012 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) : 0.5492895 object centre at (A) : 9.551999 -2.846001 44.07050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8950143E-03 4.2101678E-02 midg,1,midg; midg,igrid,midg -1.3919115E-03 9.1679636E-03 1,midg,midg; igrid,midg,midg -1.5531621E-02 -1.6587000E-02 gauss-seidel spectral radius is 0.9983522 estimated iterations to convergence 196 setup time was (sec) 0.6800000 now iterating at: 17:03:26 rms-change max change #iterations 4.074287 163.4592 at 10iterations 1.752679 60.52524 at 20iterations 0.7565129 25.12077 at 30iterations 0.3294784 10.73506 at 40iterations 0.1423941 4.900139 at 50iterations 6.1961316E-02 2.247583 at 60iterations 2.6723238E-02 0.8381882 at 70iterations 1.1597444E-02 0.3842125 at 80iterations 5.0621005E-03 0.1832304 at 90iterations 2.2017600E-03 6.9367409E-02 at 100iterations 9.5721794E-04 3.0904174E-02 at 110iterations 4.1850336E-04 1.5758514E-02 at 120iterations finished qdiffx linear iterations at : 17:03:34 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 4.1850336E-04 1.5758514E-02 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 17:03:35 8.326u 0.219s 0:09.37 91.0% 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 Mon Oct 10 2011 at 17:03:35 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 = 4055 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: 2.471803 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): -21.57800 40.68200 ymin,ymax (A): -28.22500 22.53300 zmin,zma (A): 11.66500 76.47600 x,y,z range (A): 62.26000 50.75800 64.81100 scale (grids/A): 2.471803 object centre (A): 9.551999 -2.846001 44.07050 number of atom coordinates read : 4055 total number of charged atoms : 3911 net assigned charge : 7.500031 assigned positive charge : 627.1783 centred at (gu) : 93.62935 90.84144 85.82294 assigned negative charge : -619.6826 centred at (gu) : 93.10709 90.42608 85.19026 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 200485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40757 grid for indexing accessible points = 1.400000 m= 93566 mr = 136224 m= 29245 mr = 70327 m= 5233 mr = 20722 m= 457 mr = 3022 m= 16 mr = 175 m= 1 mr = 3 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 98531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 31253 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) : 1.647869 object centre at (A) : 9.551999 -2.846001 44.07050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1369386 0.5536495 midg,1,midg; midg,igrid,midg 2.0931365E-02 8.6139493E-02 1,midg,midg; igrid,midg,midg -0.2787007 -0.3571236 gauss-seidel spectral radius is 0.9992301 estimated iterations to convergence 284 setup time was (sec) 1.300000 now iterating at: 17:03:36 rms-change max change #iterations 10.83318 391.7199 at 10iterations 6.412691 164.7412 at 20iterations 3.768198 80.07696 at 30iterations 2.194219 45.16575 at 40iterations 1.273350 24.17845 at 50iterations 0.7351530 14.58735 at 60iterations 0.4236831 8.871674 at 70iterations 0.2429521 5.040117 at 80iterations 0.1395324 2.586814 at 90iterations 7.9877235E-02 1.454554 at 100iterations 4.5616202E-02 0.9344034 at 110iterations 2.6114497E-02 0.4721069 at 120iterations 1.4908805E-02 0.3017941 at 130iterations 8.5036885E-03 0.1578112 at 140iterations 4.8520383E-03 9.1703415E-02 at 150iterations 2.7599842E-03 5.6375504E-02 at 160iterations 1.5694959E-03 2.8736115E-02 at 170iterations 8.9473196E-04 1.6550064E-02 at 180iterations finished qdiffx linear iterations at : 17:03:55 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 8.9473196E-04 1.6550064E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 17:03:56 13.575u 0.231s 0:21.80 63.3% 0+0k 0+0io 0pf+0w