Sat Oct 15 13:53:35 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 15 2011 at 13:53:35 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 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: 0.5862881 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): -8.375999 49.72100 ymin,ymax (A): -7.280000 44.40000 zmin,zma (A): 27.29300 88.01400 x,y,z range (A): 58.09700 51.68000 60.72100 scale (grids/A): 0.5862881 object centre (A): 20.67250 18.56000 57.65350 number of atom coordinates read : 2623 total number of charged atoms : 2489 net assigned charge : 12.00001 assigned positive charge : 385.7747 centred at (gu) : 89.35600 90.80028 91.51997 assigned negative charge : -373.7755 centred at (gu) : 89.26661 90.69854 91.52065 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6098 nv = 96 ne = 84 npr = 52923 no. pairs analyzed = 52923 no. exposed pairs = 3341 no. arc points = 23797 no. surface atoms = 1128 nbur = 1495 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 = 1.456000 m= 297 mr = 3172 m= 0 mr = 20 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2431 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3221074E-09 4.5500017E-09 midg,1,midg; midg,igrid,midg 7.7633733E-10 6.6370469E-09 1,midg,midg; igrid,midg,midg 1.3601205E-09 4.5302109E-09 gauss-seidel spectral radius is 0.9849585 estimated iterations to convergence 67 setup time was (sec) 0.5000000 now iterating at: 13:53:35 rms-change max change #iterations 9.7325981E-02 18.14553 at 10iterations 7.7023888E-03 1.251747 at 20iterations 6.0804054E-04 0.1238222 at 30iterations 4.8893915E-05 7.6112747E-03 at 40iterations 3.9849765E-06 6.4468384E-04 at 50iterations finished qdiffx linear iterations at : 13:53:38 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.9849765E-06 6.4468384E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 13:53:38 3.144u 0.143s 0:03.61 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 Sat Oct 15 2011 at 13:53:38 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 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: 1.758864 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): -8.375999 49.72100 ymin,ymax (A): -7.280000 44.40000 zmin,zma (A): 27.29300 88.01400 x,y,z range (A): 58.09700 51.68000 60.72100 scale (grids/A): 1.758864 object centre (A): 20.67250 18.56000 57.65350 number of atom coordinates read : 2623 total number of charged atoms : 2489 net assigned charge : 12.00001 assigned positive charge : 385.7747 centred at (gu) : 88.06721 92.40013 94.55939 assigned negative charge : -373.7755 centred at (gu) : 87.79965 92.09523 94.56179 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 21954 mr = 44948 m= 2971 mr = 15465 m= 141 mr = 1541 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 808 time to turn everything in is 0.4600000 number of dielectric boundary points 29473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19372 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) : 0.5862881 object centre at (A) : 20.67250 18.56000 57.65350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0821496E-03 9.0458449E-03 midg,1,midg; midg,igrid,midg 1.3253520E-02 3.8631041E-02 1,midg,midg; igrid,midg,midg -2.9897937E-03 4.9426374E-03 gauss-seidel spectral radius is 0.9984095 estimated iterations to convergence 199 setup time was (sec) 0.7100000 now iterating at: 13:53:39 rms-change max change #iterations 3.552516 180.2980 at 10iterations 1.557629 62.34574 at 20iterations 0.6870732 25.87497 at 30iterations 0.3026997 10.33729 at 40iterations 0.1330132 4.810724 at 50iterations 5.8612354E-02 2.049120 at 60iterations 2.5889605E-02 0.9862366 at 70iterations 1.1395581E-02 0.4468002 at 80iterations 5.0159795E-03 0.1618500 at 90iterations 2.2227319E-03 7.6625347E-02 at 100iterations 9.8134903E-04 3.4469604E-02 at 110iterations 4.3117130E-04 1.7604351E-02 at 120iterations finished qdiffx linear iterations at : 13:53:45 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 4.3117130E-04 1.7604351E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 13:53:46 6.936u 0.200s 0:07.72 92.3% 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 15 2011 at 13:53:46 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 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: 2.638296 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): -8.375999 49.72100 ymin,ymax (A): -7.280000 44.40000 zmin,zma (A): 27.29300 88.01400 x,y,z range (A): 58.09700 51.68000 60.72100 scale (grids/A): 2.638296 object centre (A): 20.67250 18.56000 57.65350 number of atom coordinates read : 2623 total number of charged atoms : 2489 net assigned charge : 12.00001 assigned positive charge : 385.7747 centred at (gu) : 87.10070 93.59991 96.83886 assigned negative charge : -373.7755 centred at (gu) : 86.69948 93.14274 96.84267 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 154230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 73705 mr = 110061 m= 24020 mr = 58880 m= 4900 mr = 18248 m= 568 mr = 3324 m= 18 mr = 299 m= 0 mr = 3 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2726 time to turn everything in is 1.130000 number of dielectric boundary points 66626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 19902 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) : 1.758864 object centre at (A) : 20.67250 18.56000 57.65350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1433902E-02 0.2233570 midg,1,midg; midg,igrid,midg 9.1886446E-02 0.4917190 1,midg,midg; igrid,midg,midg 9.3901299E-02 7.1944043E-02 gauss-seidel spectral radius is 0.9992006 estimated iterations to convergence 279 setup time was (sec) 1.410000 now iterating at: 13:53:48 rms-change max change #iterations 8.835246 310.2493 at 10iterations 5.078231 134.3735 at 20iterations 2.907573 71.74436 at 30iterations 1.645911 42.39478 at 40iterations 0.9341556 21.68694 at 50iterations 0.5279013 11.63118 at 60iterations 0.2977658 5.825692 at 70iterations 0.1679243 3.331461 at 80iterations 9.4398573E-02 1.995890 at 90iterations 5.3253990E-02 1.056534 at 100iterations 2.9933883E-02 0.7630310 at 110iterations 1.6844213E-02 0.3635626 at 120iterations 9.4935764E-03 0.1919098 at 130iterations 5.3335694E-03 0.1094939 at 140iterations 3.0086497E-03 6.0329437E-02 at 150iterations 1.6951816E-03 3.5848618E-02 at 160iterations 9.5605786E-04 2.1940231E-02 at 170iterations 5.4452178E-04 1.3610840E-02 at 180iterations finished qdiffx linear iterations at : 13:53:57 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 5.4452178E-04 1.3610840E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.17000 DelPhi exited at 13:53:58 11.174u 0.184s 0:11.89 95.4% 0+0k 0+0io 0pf+0w