Sun Oct 9 06:52:43 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 Sun Oct 9 2011 at 06:52:43 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 # of charge parameter records: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.7274362 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): -25.93800 17.51700 ymin,ymax (A): -21.44600 17.84100 zmin,zma (A): -19.55900 29.38000 x,y,z range (A): 43.45500 39.28700 48.93900 scale (grids/A): 0.7274362 object centre (A): -4.210500 -1.802500 4.910500 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 300.3760 centred at (gu) : 90.41732 90.67096 90.80084 assigned negative charge : -303.3511 centred at (gu) : 90.31462 90.81689 90.95718 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7277 nv = 96 ne = 84 npr = 41798 no. pairs analyzed = 41798 no. exposed pairs = 2483 no. arc points = 17535 no. surface atoms = 838 nbur = 1163 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 4067 m= 5 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.2600000 number of dielectric boundary points 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1481 ## 100 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4849175E-08 -1.8163226E-07 midg,1,midg; midg,igrid,midg 5.9974347E-08 -1.6806050E-07 1,midg,midg; igrid,midg,midg -1.0608494E-07 4.0739259E-08 gauss-seidel spectral radius is 0.9901432 estimated iterations to convergence 82 setup time was (sec) 0.4700000 now iterating at: 06:52:44 rms-change max change #iterations 0.2333432 31.31680 at 10iterations 3.0126581E-02 4.378624 at 20iterations 3.8732812E-03 0.5248661 at 30iterations 5.0493889E-04 7.1681976E-02 at 40iterations 6.6111475E-05 8.0261230E-03 at 50iterations finished qdiffx linear iterations at : 06:52:46 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 6.6111475E-05 8.0261230E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:52:47 3.063u 0.148s 0:03.48 91.9% 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 Sun Oct 9 2011 at 06:52:47 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.182309 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): -25.93800 17.51700 ymin,ymax (A): -21.44600 17.84100 zmin,zma (A): -19.55900 29.38000 x,y,z range (A): 43.45500 39.28700 48.93900 scale (grids/A): 2.182309 object centre (A): -4.210500 -1.802500 4.910500 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 300.3760 centred at (gu) : 91.25216 92.01277 92.40250 assigned negative charge : -303.3511 centred at (gu) : 90.94398 92.45082 92.87168 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17535 grid for indexing accessible points = 1.400000 m= 29938 mr = 53097 m= 6164 mr = 22702 m= 642 mr = 4298 m= 11 mr = 360 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2191 time to turn everything in is 0.5500000 number of dielectric boundary points 32815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 14812 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) : 0.7274362 object centre at (A) : -4.210500 -1.802500 4.910500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7255107E-02 -5.9530098E-02 midg,1,midg; midg,igrid,midg 2.8808309E-02 -1.2911571E-02 1,midg,midg; igrid,midg,midg -2.0480428E-02 -6.3470388E-03 gauss-seidel spectral radius is 0.9988844 estimated iterations to convergence 237 setup time was (sec) 0.8100000 now iterating at: 06:52:48 rms-change max change #iterations 4.849101 197.7795 at 10iterations 2.430948 77.24951 at 20iterations 1.223891 38.26666 at 30iterations 0.6185671 19.32872 at 40iterations 0.3100183 8.603931 at 50iterations 0.1561864 5.218277 at 60iterations 7.8530647E-02 2.461302 at 70iterations 3.9568808E-02 1.194744 at 80iterations 1.9916600E-02 0.6002998 at 90iterations 1.0022162E-02 0.2844915 at 100iterations 5.0609792E-03 0.1493835 at 110iterations 2.5427868E-03 6.9997787E-02 at 120iterations finished qdiffx linear iterations at : 06:52:54 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 2.5427868E-03 6.9997787E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 06:52:54 6.916u 0.154s 0:07.34 96.1% 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 Sun Oct 9 2011 at 06:52:54 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.273463 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): -25.93800 17.51700 ymin,ymax (A): -21.44600 17.84100 zmin,zma (A): -19.55900 29.38000 x,y,z range (A): 43.45500 39.28700 48.93900 scale (grids/A): 3.273463 object centre (A): -4.210500 -1.802500 4.910500 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 300.3760 centred at (gu) : 91.87817 93.01916 93.60384 assigned negative charge : -303.3511 centred at (gu) : 91.41591 93.67619 94.30751 start vw surface at 0.1300000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 176292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17535 grid for indexing accessible points = 1.400000 m= 93191 mr = 127984 m= 38263 mr = 77232 m= 11768 mr = 31679 m= 2622 mr = 9318 m= 341 mr = 2002 m= 11 mr = 209 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7229 time to turn everything in is 1.710000 number of dielectric boundary points 74062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 14880 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) : 2.182309 object centre at (A) : -4.210500 -1.802500 4.910500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1629270 -0.3757071 midg,1,midg; midg,igrid,midg 0.2722790 -3.9581407E-02 1,midg,midg; igrid,midg,midg -0.1030363 -0.1662400 gauss-seidel spectral radius is 0.9993047 estimated iterations to convergence 299 setup time was (sec) 1.990000 now iterating at: 06:52:56 rms-change max change #iterations 10.49846 371.2056 at 10iterations 6.125757 140.5213 at 20iterations 3.568777 64.85983 at 30iterations 2.083469 35.89824 at 40iterations 1.219884 25.92548 at 50iterations 0.7123470 12.10045 at 60iterations 0.4155345 7.858318 at 70iterations 0.2424938 5.422968 at 80iterations 0.1414264 2.438156 at 90iterations 8.2569405E-02 1.495605 at 100iterations 4.8208602E-02 0.7975592 at 110iterations 2.8088924E-02 0.4959002 at 120iterations 1.6373089E-02 0.2831655 at 130iterations 9.6059246E-03 0.1639709 at 140iterations 5.6000594E-03 0.1030502 at 150iterations 3.2664428E-03 5.5015564E-02 at 160iterations 1.9047334E-03 3.4454346E-02 at 170iterations 1.1123349E-03 1.8535614E-02 at 180iterations finished qdiffx linear iterations at : 06:53:06 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 1.1123349E-03 1.8535614E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 06:53:06 11.520u 0.177s 0:11.97 97.6% 0+0k 0+0io 0pf+0w