Tue Oct 11 01:56:05 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 Tue Oct 11 2011 at 01:56:05 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: GLM 264 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5464313 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): -10.72700 54.42300 ymin,ymax (A): -5.341000 46.13600 zmin,zma (A): -7.334000 35.13100 x,y,z range (A): 65.15000 51.47700 42.46500 scale (grids/A): 0.5464313 object centre (A): 21.84800 20.39750 13.89850 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 6.906014 assigned positive charge : 384.3401 centred at (gu) : 91.75563 89.38769 89.77498 assigned negative charge : -377.4345 centred at (gu) : 91.62688 89.32071 89.90965 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4849 nv = 96 ne = 84 npr = 52349 no. pairs analyzed = 52349 no. exposed pairs = 3078 no. arc points = 21630 no. surface atoms = 1033 nbur = 1526 mkacc time = 0.1200000 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 = 1.568000 m= 184 mr = 2567 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3300000 number of dielectric boundary points 2460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2167 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2482176E-09 -3.3906913E-10 midg,1,midg; midg,igrid,midg 3.9579201E-11 6.9158934E-10 1,midg,midg; igrid,midg,midg -2.0396117E-10 1.7795878E-09 gauss-seidel spectral radius is 0.9826943 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 01:56:06 rms-change max change #iterations 7.2141595E-02 13.23269 at 10iterations 5.5852765E-03 1.164215 at 20iterations 7.1314897E-04 0.1872101 at 30iterations 1.4735400E-04 3.9882660E-02 at 40iterations 3.2101165E-05 8.8272095E-03 at 50iterations finished qdiffx linear iterations at : 01:56:08 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 3.2101165E-05 8.8272095E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 01:56:09 3.340u 0.145s 0:03.88 89.6% 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 Tue Oct 11 2011 at 01:56:09 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: GLM 264 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.639294 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): -10.72700 54.42300 ymin,ymax (A): -5.341000 46.13600 zmin,zma (A): -7.334000 35.13100 x,y,z range (A): 65.15000 51.47700 42.46500 scale (grids/A): 1.639294 object centre (A): 21.84800 20.39750 13.89850 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 6.906014 assigned positive charge : 384.3401 centred at (gu) : 95.26669 88.16248 89.32455 assigned negative charge : -377.4345 centred at (gu) : 94.88057 87.96179 89.72861 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 54216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21630 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15687 mr = 37199 m= 1473 mr = 10734 m= 20 mr = 733 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2148 time to turn everything in is 0.4300000 number of dielectric boundary points 22730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18498 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) : 0.5464313 object centre at (A) : 21.84800 20.39750 13.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0004767E-02 1.6388915E-03 midg,1,midg; midg,igrid,midg 6.7372955E-03 1.1331444E-02 1,midg,midg; igrid,midg,midg -1.7763588E-04 -9.4371662E-03 gauss-seidel spectral radius is 0.9981456 estimated iterations to convergence 185 setup time was (sec) 0.7100000 now iterating at: 01:56:10 rms-change max change #iterations 3.058716 138.9021 at 10iterations 1.262743 51.99108 at 20iterations 0.5200687 22.14536 at 30iterations 0.2150532 8.294741 at 40iterations 8.9197576E-02 3.420189 at 50iterations 3.6897231E-02 1.496974 at 60iterations 1.5403696E-02 0.6229897 at 70iterations 6.4863800E-03 0.2725563 at 80iterations 2.7867325E-03 0.1169739 at 90iterations 1.2545752E-03 5.6201935E-02 at 100iterations 6.0333830E-04 3.0151367E-02 at 110iterations 3.0698173E-04 1.7005920E-02 at 120iterations finished qdiffx linear iterations at : 01:56:16 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 3.0698173E-04 1.7005920E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 01:56:17 7.201u 0.161s 0:07.75 94.9% 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 01:56:17 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: GLM 264 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.458941 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): -10.72700 54.42300 ymin,ymax (A): -5.341000 46.13600 zmin,zma (A): -7.334000 35.13100 x,y,z range (A): 65.15000 51.47700 42.46500 scale (grids/A): 2.458941 object centre (A): 21.84800 20.39750 13.89850 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 6.906014 assigned positive charge : 384.3401 centred at (gu) : 97.89973 87.24353 88.98681 assigned negative charge : -377.4345 centred at (gu) : 97.32070 86.94263 89.59283 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 126170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21630 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 55642 mr = 90846 m= 14685 mr = 44181 m= 2203 mr = 11021 m= 118 mr = 1430 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 7438 time to turn everything in is 0.9600000 number of dielectric boundary points 51298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19314 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) : 1.639294 object centre at (A) : 21.84800 20.39750 13.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1227835 2.7655648E-02 midg,1,midg; midg,igrid,midg 0.1357959 0.1696387 1,midg,midg; igrid,midg,midg -4.6959482E-02 -0.2128477 gauss-seidel spectral radius is 0.9991082 estimated iterations to convergence 265 setup time was (sec) 1.260000 now iterating at: 01:56:18 rms-change max change #iterations 7.784608 262.5941 at 10iterations 4.281538 140.7425 at 20iterations 2.347352 59.51775 at 30iterations 1.276451 28.25938 at 40iterations 0.6958384 15.63087 at 50iterations 0.3793166 8.141083 at 60iterations 0.2065941 4.738417 at 70iterations 0.1124767 2.676258 at 80iterations 6.1138857E-02 1.362979 at 90iterations 3.3320684E-02 0.8297367 at 100iterations 1.8177865E-02 0.4347229 at 110iterations 9.9260118E-03 0.2362404 at 120iterations 5.4687639E-03 0.1406403 at 130iterations 3.0373784E-03 7.9139709E-02 at 140iterations 1.7186807E-03 4.7351837E-02 at 150iterations 1.0034731E-03 2.9342651E-02 at 160iterations 6.0622889E-04 1.8173218E-02 at 170iterations 3.8409117E-04 1.2420654E-02 at 180iterations finished qdiffx linear iterations at : 01:56:28 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 3.8409117E-04 1.2420654E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 01:56:29 11.272u 0.161s 0:12.18 93.8% 0+0k 0+0io 0pf+0w