Tue Oct 11 01:14:13 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 01:14:13 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 = 2733 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.5624368 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): -31.95000 19.85600 ymin,ymax (A): 17.50300 80.79900 zmin,zma (A): 16.96600 59.78900 x,y,z range (A): 51.80600 63.29601 42.82300 scale (grids/A): 0.5624368 object centre (A): -6.047000 49.15100 38.37750 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.500017 assigned positive charge : 413.8515 centred at (gu) : 88.47491 88.76123 90.07648 assigned negative charge : -409.3522 centred at (gu) : 88.53944 88.93935 89.92181 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5553 nv = 96 ne = 84 npr = 55390 no. pairs analyzed = 55390 no. exposed pairs = 3263 no. arc points = 22755 no. surface atoms = 1102 nbur = 1631 mkacc time = 0.1000000 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= 192 mr = 3011 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2100000 number of dielectric boundary points 2732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2238 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7116 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2392205E-09 2.2068714E-09 midg,1,midg; midg,igrid,midg 3.2696119E-09 -1.1286915E-09 1,midg,midg; igrid,midg,midg 1.7272841E-09 -1.5707012E-10 gauss-seidel spectral radius is 0.9836668 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 01:14:13 rms-change max change #iterations 8.3449937E-02 14.77545 at 10iterations 6.7657554E-03 1.227415 at 20iterations 9.0385403E-04 0.2271843 at 30iterations 2.2139787E-04 6.1752319E-02 at 40iterations 6.0599552E-05 1.6902924E-02 at 50iterations finished qdiffx linear iterations at : 01:14:16 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.0599552E-05 1.6902924E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 01:14:17 3.456u 0.160s 0:04.09 88.2% 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 Tue Oct 11 2011 at 01:14:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.687310 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): -31.95000 19.85600 ymin,ymax (A): 17.50300 80.79900 zmin,zma (A): 16.96600 59.78900 x,y,z range (A): 51.80600 63.29601 42.82300 scale (grids/A): 1.687310 object centre (A): -6.047000 49.15100 38.37750 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.500017 assigned positive charge : 413.8515 centred at (gu) : 85.42384 86.28316 90.22855 assigned negative charge : -409.3522 centred at (gu) : 85.61799 86.81747 89.76519 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22755 grid for indexing accessible points = 1.400000 m= 19084 mr = 43375 m= 2079 mr = 13676 m= 60 mr = 1086 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2564 time to turn everything in is 0.3200000 number of dielectric boundary points 25281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19986 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) : 0.5624368 object centre at (A) : -6.047000 49.15100 38.37750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4819643E-03 1.4670749E-02 midg,1,midg; midg,igrid,midg -1.0106936E-02 -1.6478522E-02 1,midg,midg; igrid,midg,midg 7.1045529E-04 -8.3070787E-05 gauss-seidel spectral radius is 0.9982697 estimated iterations to convergence 191 setup time was (sec) 0.5400000 now iterating at: 01:14:17 rms-change max change #iterations 3.365242 155.8146 at 10iterations 1.429407 52.52080 at 20iterations 0.6090416 23.20606 at 30iterations 0.2607056 9.710384 at 40iterations 0.1108916 4.110058 at 50iterations 4.7524955E-02 1.691363 at 60iterations 2.0268638E-02 0.7847786 at 70iterations 8.7374290E-03 0.3266766 at 80iterations 3.8417452E-03 0.1394157 at 90iterations 1.7400477E-03 7.3066711E-02 at 100iterations 8.3259284E-04 3.9449215E-02 at 110iterations 4.1823322E-04 2.0343781E-02 at 120iterations finished qdiffx linear iterations at : 01:14:25 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 4.1823322E-04 2.0343781E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 01:14:25 7.780u 0.190s 0:08.31 95.9% 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 01:14:25 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 = 2733 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.530965 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): -31.95000 19.85600 ymin,ymax (A): 17.50300 80.79900 zmin,zma (A): 16.96600 59.78900 x,y,z range (A): 51.80600 63.29601 42.82300 scale (grids/A): 2.530965 object centre (A): -6.047000 49.15100 38.37750 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.500017 assigned positive charge : 413.8515 centred at (gu) : 83.13561 84.42471 90.34261 assigned negative charge : -409.3522 centred at (gu) : 83.42691 85.22614 89.64763 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 144614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22755 grid for indexing accessible points = 1.400000 m= 67101 mr = 106043 m= 19180 mr = 54202 m= 3340 mr = 14864 m= 206 mr = 2254 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 9073 time to turn everything in is 0.7400000 number of dielectric boundary points 56989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20703 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) : 1.687310 object centre at (A) : -6.047000 49.15100 38.37750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8164254E-02 0.1856811 midg,1,midg; midg,igrid,midg -0.6012320 -0.3282645 1,midg,midg; igrid,midg,midg -4.4200379E-02 -3.5809632E-02 gauss-seidel spectral radius is 0.9991490 estimated iterations to convergence 271 setup time was (sec) 0.9600000 now iterating at: 01:14:26 rms-change max change #iterations 8.420366 304.9802 at 10iterations 4.666003 128.5919 at 20iterations 2.584082 66.00190 at 30iterations 1.430606 34.97088 at 40iterations 0.7917656 20.41727 at 50iterations 0.4372750 10.80630 at 60iterations 0.2413577 5.510452 at 70iterations 0.1332590 2.743998 at 80iterations 7.3625833E-02 1.532219 at 90iterations 4.0669210E-02 0.8480034 at 100iterations 2.2387523E-02 0.4682426 at 110iterations 1.2393510E-02 0.2575760 at 120iterations 6.8869507E-03 0.1594238 at 130iterations 3.8450479E-03 8.0352783E-02 at 140iterations 2.1788238E-03 4.7901154E-02 at 150iterations 1.2568295E-03 3.0933380E-02 at 160iterations 7.5013418E-04 1.8421173E-02 at 170iterations 4.6384009E-04 1.2798309E-02 at 180iterations finished qdiffx linear iterations at : 01:14:37 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 4.6384009E-04 1.2798309E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 01:14:38 12.205u 0.208s 0:12.78 97.0% 0+0k 0+0io 0pf+0w