Mon Oct 10 18:50:07 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 Mon Oct 10 2011 at 18:50:07 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: SEP 33 has a net charge of -0.4750 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 0.5747591 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): -14.10900 47.83000 ymin,ymax (A): 60.24600 115.6350 zmin,zma (A): 44.23400 87.93900 x,y,z range (A): 61.93900 55.38900 43.70501 scale (grids/A): 0.5747591 object centre (A): 16.86050 87.94050 66.08650 number of atom coordinates read : 2585 total number of charged atoms : 2484 net assigned charge : 0.5530079 assigned positive charge : 402.0644 centred at (gu) : 87.73432 91.30009 91.08465 assigned negative charge : -401.5123 centred at (gu) : 87.83144 91.35587 91.22240 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5659 nv = 96 ne = 84 npr = 50750 no. pairs analyzed = 50750 no. exposed pairs = 3262 no. arc points = 22438 no. surface atoms = 1082 nbur = 1503 mkacc time = 0.1100000 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= 271 mr = 3096 m= 0 mr = 19 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8088301E-09 -2.8777158E-09 midg,1,midg; midg,igrid,midg 7.4810175E-10 -1.1331156E-09 1,midg,midg; igrid,midg,midg 2.9282881E-09 -8.8704893E-10 gauss-seidel spectral radius is 0.9843442 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 18:50:08 rms-change max change #iterations 8.8292360E-02 13.41507 at 10iterations 7.0206043E-03 1.233902 at 20iterations 6.4467406E-04 0.1020508 at 30iterations 1.1302228E-04 2.1601200E-02 at 40iterations 2.9208679E-05 5.8140755E-03 at 50iterations finished qdiffx linear iterations at : 18:50:10 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.9208679E-05 5.8140755E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 18:50:11 3.117u 0.159s 0:03.59 90.8% 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 18:50:11 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: SEP 33 has a net charge of -0.4750 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 1.724277 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): -14.10900 47.83000 ymin,ymax (A): 60.24600 115.6350 zmin,zma (A): 44.23400 87.93900 x,y,z range (A): 61.93900 55.38900 43.70501 scale (grids/A): 1.724277 object centre (A): 16.86050 87.94050 66.08650 number of atom coordinates read : 2585 total number of charged atoms : 2484 net assigned charge : 0.5530079 assigned positive charge : 402.0644 centred at (gu) : 83.20184 93.89960 93.25320 assigned negative charge : -401.5123 centred at (gu) : 83.49403 94.06742 93.66679 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22438 grid for indexing accessible points = 1.400000 m= 21455 mr = 43629 m= 2673 mr = 15567 m= 92 mr = 1512 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 272 time to turn everything in is 0.4500000 number of dielectric boundary points 26092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19244 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) : 0.5747591 object centre at (A) : 16.86050 87.94050 66.08650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9131049E-03 -8.4017916E-03 midg,1,midg; midg,igrid,midg 1.6033221E-02 -1.1439878E-02 1,midg,midg; igrid,midg,midg 1.7397111E-02 -1.2033704E-02 gauss-seidel spectral radius is 0.9983316 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 18:50:12 rms-change max change #iterations 3.508023 216.9296 at 10iterations 1.512531 64.80676 at 20iterations 0.6530649 24.24177 at 30iterations 0.2834531 10.19930 at 40iterations 0.1220039 4.010700 at 50iterations 5.2896012E-02 1.913611 at 60iterations 2.2951504E-02 0.8847890 at 70iterations 9.8954486E-03 0.3927259 at 80iterations 4.3266304E-03 0.1598835 at 90iterations 1.8945057E-03 6.9238663E-02 at 100iterations 8.3579140E-04 2.9554605E-02 at 110iterations 3.7607437E-04 1.3614655E-02 at 120iterations finished qdiffx linear iterations at : 18:50:18 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 3.7607437E-04 1.3614655E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.830000 DelPhi exited at 18:50:18 6.834u 0.179s 0:07.46 93.8% 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 18:50:18 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: SEP 33 has a net charge of -0.4750 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 2.586416 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): -14.10900 47.83000 ymin,ymax (A): 60.24600 115.6350 zmin,zma (A): 44.23400 87.93900 x,y,z range (A): 61.93900 55.38900 43.70501 scale (grids/A): 2.586416 object centre (A): 16.86050 87.94050 66.08650 number of atom coordinates read : 2585 total number of charged atoms : 2484 net assigned charge : 0.5530079 assigned positive charge : 402.0644 centred at (gu) : 79.80267 95.84946 94.87960 assigned negative charge : -401.5123 centred at (gu) : 80.24089 96.10115 95.50008 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 145301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22438 grid for indexing accessible points = 1.400000 m= 71624 mr = 106324 m= 23622 mr = 58301 m= 4489 mr = 18616 m= 387 mr = 3179 m= 5 mr = 213 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 931 time to turn everything in is 1.040000 number of dielectric boundary points 58793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 19858 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) : 1.724277 object centre at (A) : 16.86050 87.94050 66.08650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0122807E-02 -8.6684071E-02 midg,1,midg; midg,igrid,midg 0.2811601 -0.1884994 1,midg,midg; igrid,midg,midg 0.5286963 4.1608344E-04 gauss-seidel spectral radius is 0.9991699 estimated iterations to convergence 274 setup time was (sec) 1.320000 now iterating at: 18:50:20 rms-change max change #iterations 8.923376 271.8708 at 10iterations 5.074398 153.8850 at 20iterations 2.876919 77.11673 at 30iterations 1.622611 42.23709 at 40iterations 0.9106687 20.22497 at 50iterations 0.5108494 13.54782 at 60iterations 0.2851959 5.973900 at 70iterations 0.1597573 3.439532 at 80iterations 8.9188069E-02 2.016239 at 90iterations 4.9809739E-02 1.032612 at 100iterations 2.7683601E-02 0.5999508 at 110iterations 1.5444756E-02 0.3250427 at 120iterations 8.6169681E-03 0.2016425 at 130iterations 4.7874502E-03 0.1123306 at 140iterations 2.6533490E-03 5.8551311E-02 at 150iterations 1.4836353E-03 2.9971123E-02 at 160iterations 8.2432327E-04 1.7116547E-02 at 170iterations 4.5914456E-04 9.6492767E-03 at 180iterations finished qdiffx linear iterations at : 18:50:29 total time elapsed so far: 10.75000 # loops : 180 mean,max change (kT/e) : 4.5914456E-04 9.6492767E-03 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.93000 DelPhi exited at 18:50:30 10.930u 0.171s 0:11.47 96.7% 0+0k 0+0io 0pf+0w