Sat Oct 8 15:58:15 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+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 Sat Oct 8 2011 at 15:58:15 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2369 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5827372 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): -2.272000 46.19500 ymin,ymax (A): -15.82700 29.79300 zmin,zma (A): -19.20800 41.88300 x,y,z range (A): 48.46700 45.62000 61.09100 scale (grids/A): 0.5827372 object centre (A): 21.96150 6.983000 11.33750 number of atom coordinates read : 2369 total number of charged atoms : 2284 net assigned charge : 3.806002 assigned positive charge : 354.4140 centred at (gu) : 90.27316 88.85629 88.85815 assigned negative charge : -350.6088 centred at (gu) : 90.29977 88.98626 88.88505 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5192 nv = 96 ne = 84 npr = 48377 no. pairs analyzed = 48377 no. exposed pairs = 2934 no. arc points = 20532 no. surface atoms = 1003 nbur = 1366 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 = 1.484000 m= 218 mr = 2728 m= 0 mr = 16 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3100000 number of dielectric boundary points 2666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6755 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8041934E-09 2.8848449E-10 midg,1,midg; midg,igrid,midg 4.3266217E-09 -1.2320259E-09 1,midg,midg; igrid,midg,midg 1.2961736E-09 3.9266837E-10 gauss-seidel spectral radius is 0.9847463 estimated iterations to convergence 66 setup time was (sec) 0.6100000 now iterating at: 15:58:16 rms-change max change #iterations 9.1129042E-02 18.54720 at 10iterations 7.1630268E-03 1.450581 at 20iterations 6.0833746E-04 0.1011658 at 30iterations 7.2547104E-05 1.2971401E-02 at 40iterations 1.4608419E-05 3.0364990E-03 at 50iterations finished qdiffx linear iterations at : 15:58:19 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.4608419E-05 3.0364990E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 15:58:20 4.280u 0.266s 0:04.87 93.2% 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 Sat Oct 8 2011 at 15:58:20 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2369 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.748212 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): -2.272000 46.19500 ymin,ymax (A): -15.82700 29.79300 zmin,zma (A): -19.20800 41.88300 x,y,z range (A): 48.46700 45.62000 61.09100 scale (grids/A): 1.748212 object centre (A): 21.96150 6.983000 11.33750 number of atom coordinates read : 2369 total number of charged atoms : 2284 net assigned charge : 3.806002 assigned positive charge : 354.4140 centred at (gu) : 90.81916 86.56833 86.57388 assigned negative charge : -350.6088 centred at (gu) : 90.89919 86.95874 86.65524 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20532 grid for indexing accessible points = 1.400000 m= 18450 mr = 39401 m= 2443 mr = 13129 m= 89 mr = 1419 m= 0 mr = 18 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 693 time to turn everything in is 0.4600000 number of dielectric boundary points 24598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 17762 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) : 0.5827372 object centre at (A) : 21.96150 6.983000 11.33750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7951911E-02 1.5848834E-02 midg,1,midg; midg,igrid,midg 1.2697574E-02 -2.3166703E-03 1,midg,midg; igrid,midg,midg 3.0381163E-03 -1.5129952E-02 gauss-seidel spectral radius is 0.9983544 estimated iterations to convergence 196 setup time was (sec) 0.8100000 now iterating at: 15:58:21 rms-change max change #iterations 3.374157 152.9432 at 10iterations 1.470425 63.29346 at 20iterations 0.6407165 24.48766 at 30iterations 0.2783601 10.64124 at 40iterations 0.1217295 4.462801 at 50iterations 5.3049471E-02 1.949459 at 60iterations 2.3040427E-02 0.8189278 at 70iterations 1.0018870E-02 0.3686409 at 80iterations 4.3852790E-03 0.1593781 at 90iterations 1.9069125E-03 6.9650650E-02 at 100iterations 8.3038781E-04 2.9031038E-02 at 110iterations 3.6317116E-04 1.2620926E-02 at 120iterations finished qdiffx linear iterations at : 15:58:30 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 3.6317116E-04 1.2620926E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 15:58:30 9.510u 0.292s 0:10.10 97.0% 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 Sat Oct 8 2011 at 15:58:30 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2369 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.622317 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): -2.272000 46.19500 ymin,ymax (A): -15.82700 29.79300 zmin,zma (A): -19.20800 41.88300 x,y,z range (A): 48.46700 45.62000 61.09100 scale (grids/A): 2.622317 object centre (A): 21.96150 6.983000 11.33750 number of atom coordinates read : 2369 total number of charged atoms : 2284 net assigned charge : 3.806002 assigned positive charge : 354.4140 centred at (gu) : 91.22859 84.85259 84.86068 assigned negative charge : -350.6088 centred at (gu) : 91.34876 85.43809 84.98290 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 133709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20532 grid for indexing accessible points = 1.400000 m= 62388 mr = 96292 m= 19902 mr = 49839 m= 4051 mr = 15721 m= 376 mr = 2990 m= 8 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 2234 time to turn everything in is 1.130000 number of dielectric boundary points 55393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 18264 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) : 1.748212 object centre at (A) : 21.96150 6.983000 11.33750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2421274 0.5008690 midg,1,midg; midg,igrid,midg 0.1416651 -3.7492517E-02 1,midg,midg; igrid,midg,midg 4.6971779E-02 -0.2694514 gauss-seidel spectral radius is 0.9991745 estimated iterations to convergence 275 setup time was (sec) 1.490000 now iterating at: 15:58:32 rms-change max change #iterations 8.391168 237.8151 at 10iterations 4.766598 127.0552 at 20iterations 2.696530 66.86117 at 30iterations 1.522739 33.63735 at 40iterations 0.8550109 18.82921 at 50iterations 0.4811640 10.72346 at 60iterations 0.2694325 6.466688 at 70iterations 0.1509001 3.307850 at 80iterations 8.4246762E-02 1.934368 at 90iterations 4.7016017E-02 0.9757462 at 100iterations 2.6297692E-02 0.6006527 at 110iterations 1.4708522E-02 0.2995625 at 120iterations 8.1995791E-03 0.1730617 at 130iterations 4.5828889E-03 0.1024246 at 140iterations 2.5611459E-03 5.4412842E-02 at 150iterations 1.4282711E-03 3.1280518E-02 at 160iterations 8.0369192E-04 1.9115925E-02 at 170iterations 4.5222440E-04 9.4871521E-03 at 180iterations finished qdiffx linear iterations at : 15:58:46 total time elapsed so far: 15.66000 # loops : 180 mean,max change (kT/e) : 4.5222440E-04 9.4871521E-03 energy calculations done at 15.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 15:58:47 15.851u 0.352s 0:16.49 98.2% 0+0k 0+0io 0pf+0w