Wed Feb 15 08:53:59 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:01 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 0.7481349 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 0.7481349 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 89.07200 90.41683 90.25998 assigned negative charge : -322.8520 centred at (gu) : 89.10596 90.49541 90.43835 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8129 nv = 96 ne = 84 npr = 44416 no. pairs analyzed = 44416 no. exposed pairs = 2752 no. arc points = 19164 no. surface atoms = 929 nbur = 1186 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 588 mr = 4455 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.1800000 number of dielectric boundary points 4150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1495 ## 105 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2189999E-08 -3.6090057E-07 midg,1,midg; midg,igrid,midg -2.9017997E-08 -2.3800179E-07 1,midg,midg; igrid,midg,midg -9.8706707E-08 -1.4046230E-07 gauss-seidel spectral radius is 0.9906898 estimated iterations to convergence 84 setup time was (sec) 0.3700000 now iterating at: 08:54:01 rms-change max change #iterations 0.2587117 38.57871 at 10iterations 3.5351209E-02 4.442157 at 20iterations 4.8668324E-03 0.5817878 at 30iterations 6.5994402E-04 8.5778713E-02 at 40iterations 9.2490896E-05 1.2369156E-02 at 50iterations finished qdiffx linear iterations at : 08:54:04 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 9.2490896E-05 1.2369156E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 08:54:05 3.436u 0.176s 0:05.46 65.9% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:54:06 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 2.244405 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 2.244405 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 87.21589 91.25055 90.78004 assigned negative charge : -322.8520 centred at (gu) : 87.31781 91.48618 91.31506 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84962 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19164 grid for indexing accessible points = 1.400000 m= 34471 mr = 58154 m= 7678 mr = 26039 m= 849 mr = 5230 m= 35 mr = 470 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1983 time to turn everything in is 0.4400000 number of dielectric boundary points 38102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15766 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) : 0.7481349 object centre at (A) : 1.659500 14.13850 20.29550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2355503E-03 -0.1400880 midg,1,midg; midg,igrid,midg -2.6392139E-02 -3.0933185E-02 1,midg,midg; igrid,midg,midg -1.3863705E-02 -1.0199012E-02 gauss-seidel spectral radius is 0.9989474 estimated iterations to convergence 244 setup time was (sec) 0.6600000 now iterating at: 08:54:07 rms-change max change #iterations 5.211018 218.6547 at 10iterations 2.660921 80.21703 at 20iterations 1.362699 38.71787 at 30iterations 0.6987662 19.85863 at 40iterations 0.3588883 10.24158 at 50iterations 0.1844225 4.989334 at 60iterations 9.4486117E-02 2.946856 at 70iterations 4.8220243E-02 1.370087 at 80iterations 2.4815779E-02 0.6455917 at 90iterations 1.2755467E-02 0.3692762 at 100iterations 6.5364596E-03 0.1825705 at 110iterations 3.3505610E-03 9.6664429E-02 at 120iterations finished qdiffx linear iterations at : 08:54:14 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 3.3505610E-03 9.6664429E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 08:54:15 8.101u 0.218s 0:08.70 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 Wed Feb 15 2012 at 08:54:15 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 3.366607 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 3.366607 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 85.82385 91.87578 91.17007 assigned negative charge : -322.8520 centred at (gu) : 85.97677 92.22931 91.97270 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 195652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19164 grid for indexing accessible points = 1.400000 m= 104714 mr = 140411 m= 45686 mr = 86335 m= 14807 mr = 37738 m= 3508 mr = 11598 m= 461 mr = 2595 m= 24 mr = 269 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 6486 time to turn everything in is 1.350000 number of dielectric boundary points 85902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 15808 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) : 2.244405 object centre at (A) : 1.659500 14.13850 20.29550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6154547E-02 -1.226788 midg,1,midg; midg,igrid,midg -0.2456756 -0.1641818 1,midg,midg; igrid,midg,midg -0.1779429 -0.1555860 gauss-seidel spectral radius is 0.9993292 estimated iterations to convergence 305 setup time was (sec) 1.590000 now iterating at: 08:54:17 rms-change max change #iterations 11.22862 306.6482 at 10iterations 6.649360 144.9122 at 20iterations 3.948216 92.45666 at 30iterations 2.336827 42.86225 at 40iterations 1.379926 23.12505 at 50iterations 0.8155383 13.58381 at 60iterations 0.4818929 7.930812 at 70iterations 0.2838102 4.531952 at 80iterations 0.1673867 2.735665 at 90iterations 9.9023640E-02 1.828670 at 100iterations 5.8305126E-02 0.8939402 at 110iterations 3.4345999E-02 0.6281204 at 120iterations 2.0275597E-02 0.3292775 at 130iterations 1.1941209E-02 0.1931963 at 140iterations 7.0576989E-03 0.1206999 at 150iterations 4.1596163E-03 7.0014000E-02 at 160iterations 2.4543868E-03 3.9398193E-02 at 170iterations 1.4430014E-03 2.2335768E-02 at 180iterations finished qdiffx linear iterations at : 08:54:30 total time elapsed so far: 14.33000 # loops : 180 mean,max change (kT/e) : 1.4430014E-03 2.2335768E-02 energy calculations done at 14.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.46000 DelPhi exited at 08:54:30 14.458u 0.229s 0:15.24 96.2% 0+0k 0+0io 0pf+0w