Wed Feb 15 08:54:33 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 08:54:34 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: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 0.6086094 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 0.6086094 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000003 assigned positive charge : 290.5330 centred at (gu) : 90.28216 90.36544 89.56400 assigned negative charge : -287.5333 centred at (gu) : 90.29170 90.48489 89.40223 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4892 nv = 96 ne = 84 npr = 40300 no. pairs analyzed = 40300 no. exposed pairs = 2551 no. arc points = 17922 no. surface atoms = 861 nbur = 1104 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 222 mr = 2609 m= 0 mr = 13 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1700000 number of dielectric boundary points 2492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1913 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4815307E-09 6.6489694E-09 midg,1,midg; midg,igrid,midg 5.4286922E-09 -2.7366891E-09 1,midg,midg; igrid,midg,midg 1.9595969E-09 1.5010027E-09 gauss-seidel spectral radius is 0.9859706 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 08:54:34 rms-change max change #iterations 9.8674662E-02 17.43729 at 10iterations 8.5301483E-03 1.443953 at 20iterations 7.5751508E-04 0.1208153 at 30iterations 6.4754116E-05 1.4439583E-02 at 40iterations 5.6666536E-06 9.8419189E-04 at 50iterations finished qdiffx linear iterations at : 08:54:38 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 5.6666536E-06 9.8419189E-04 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 08:54:39 4.129u 0.282s 0:09.38 46.9% 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 Wed Feb 15 2012 at 08:54:43 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: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 1.825828 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 1.825828 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000003 assigned positive charge : 290.5330 centred at (gu) : 90.84625 91.09647 88.69244 assigned negative charge : -287.5333 centred at (gu) : 90.87537 91.45477 88.20686 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 53139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17922 grid for indexing accessible points = 1.400000 m= 18495 mr = 36020 m= 2425 mr = 13639 m= 75 mr = 1464 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1133 time to turn everything in is 0.2800000 number of dielectric boundary points 22996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14350 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) : 0.6086094 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4605729E-03 1.1939575E-02 midg,1,midg; midg,igrid,midg 6.5715821E-03 -4.1890801E-03 1,midg,midg; igrid,midg,midg 3.3419900E-02 3.1206669E-02 gauss-seidel spectral radius is 0.9984406 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 08:54:44 rms-change max change #iterations 3.322211 165.2229 at 10iterations 1.471436 59.79525 at 20iterations 0.6523110 24.22981 at 30iterations 0.2900603 12.73694 at 40iterations 0.1292963 4.851405 at 50iterations 5.7433233E-02 2.079060 at 60iterations 2.5325945E-02 0.9647865 at 70iterations 1.1296325E-02 0.4258623 at 80iterations 5.0149178E-03 0.1827831 at 90iterations 2.2362147E-03 8.2598686E-02 at 100iterations 9.9052757E-04 3.3569932E-02 at 110iterations 4.4162286E-04 1.8941879E-02 at 120iterations finished qdiffx linear iterations at : 08:54:53 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 4.4162286E-04 1.8941879E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 08:54:56 9.346u 0.317s 0:13.32 72.4% 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 08:54:56 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: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 2.738742 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 2.738742 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000003 assigned positive charge : 290.5330 centred at (gu) : 91.26945 91.64468 88.03875 assigned negative charge : -287.5333 centred at (gu) : 91.31303 92.18217 87.31042 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 122820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17922 grid for indexing accessible points = 1.400000 m= 60748 mr = 87285 m= 20602 mr = 49686 m= 4163 mr = 16622 m= 388 mr = 3056 m= 8 mr = 224 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3746 time to turn everything in is 0.7000000 number of dielectric boundary points 51856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14662 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) : 1.825828 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4563801E-02 0.1094786 midg,1,midg; midg,igrid,midg 4.9021620E-02 -3.7971523E-02 1,midg,midg; igrid,midg,midg 0.3738751 0.3405375 gauss-seidel spectral radius is 0.9991901 estimated iterations to convergence 277 setup time was (sec) 0.9500000 now iterating at: 08:54:58 rms-change max change #iterations 7.977928 342.3361 at 10iterations 4.531114 127.3855 at 20iterations 2.557897 62.94055 at 30iterations 1.431707 38.95785 at 40iterations 0.8032517 24.23185 at 50iterations 0.4491362 9.831047 at 60iterations 0.2516304 5.802109 at 70iterations 0.1404696 3.333994 at 80iterations 7.8672245E-02 1.710803 at 90iterations 4.3947686E-02 1.008980 at 100iterations 2.4490418E-02 0.5488491 at 110iterations 1.3715154E-02 0.2756076 at 120iterations 7.6615410E-03 0.1576939 at 130iterations 4.2784433E-03 9.6340179E-02 at 140iterations 2.3972380E-03 5.6904793E-02 at 150iterations 1.3352680E-03 2.7956009E-02 at 160iterations 7.4453128E-04 1.6485453E-02 at 170iterations 4.1631577E-04 9.4146729E-03 at 180iterations finished qdiffx linear iterations at : 08:55:10 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 4.1631577E-04 9.4146729E-03 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 08:55:11 13.247u 0.389s 0:14.04 97.0% 0+0k 0+0io 0pf+0w