Wed Dec 28 11:02:19 PST 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 Wed Dec 28 2011 at 11:02:19 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6062773 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): 1.924000 44.61600 ymin,ymax (A): -24.24600 24.44600 zmin,zma (A): -28.91100 29.80800 x,y,z range (A): 42.69200 48.69200 58.71900 scale (grids/A): 0.6062773 object centre (A): 23.27000 9.9999428E-02 0.4485006 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 290.6260 centred at (gu) : 90.11530 89.93306 89.73391 assigned negative charge : -288.6263 centred at (gu) : 90.31602 89.93127 89.71960 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4892 nv = 96 ne = 84 npr = 39858 no. pairs analyzed = 39858 no. exposed pairs = 2402 no. arc points = 17202 no. surface atoms = 817 nbur = 1147 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 242 mr = 2710 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 5971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2896899E-10 1.4495020E-09 midg,1,midg; midg,igrid,midg 1.0228725E-09 1.1092911E-09 1,midg,midg; igrid,midg,midg 7.3303146E-09 -5.8492953E-09 gauss-seidel spectral radius is 0.9858638 estimated iterations to convergence 69 setup time was (sec) 0.8100000 now iterating at: 11:02:21 rms-change max change #iterations 9.8857932E-02 17.62198 at 10iterations 8.4389420E-03 1.445667 at 20iterations 7.4609485E-04 0.1222687 at 30iterations 6.4805718E-05 1.1633873E-02 at 40iterations 5.5787318E-06 9.4866753E-04 at 50iterations finished qdiffx linear iterations at : 11:02:28 total time elapsed so far: 7.520000 # loops : 50 mean,max change (kT/e) : 5.5787318E-06 9.4866753E-04 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 11:02:29 7.692u 0.687s 0:10.08 83.0% 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 Dec 28 2011 at 11:02:29 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.818832 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): 1.924000 44.61600 ymin,ymax (A): -24.24600 24.44600 zmin,zma (A): -28.91100 29.80800 x,y,z range (A): 42.69200 48.69200 58.71900 scale (grids/A): 1.818832 object centre (A): 23.27000 9.9999428E-02 0.4485006 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 290.6260 centred at (gu) : 90.34580 89.79905 89.20174 assigned negative charge : -288.6263 centred at (gu) : 90.94818 89.79408 89.15879 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 53114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17202 grid for indexing accessible points = 1.400000 m= 19150 mr = 36711 m= 2402 mr = 14528 m= 76 mr = 1395 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 22096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14336 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) : 0.6062773 object centre at (A) : 23.27000 9.9999428E-02 0.4485006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0154389E-02 2.3849774E-02 midg,1,midg; midg,igrid,midg -1.2791432E-03 -1.8600489E-03 1,midg,midg; igrid,midg,midg 8.8718524E-03 -1.5378187E-02 gauss-seidel spectral radius is 0.9984295 estimated iterations to convergence 200 setup time was (sec) 1.010000 now iterating at: 11:02:31 rms-change max change #iterations 3.275601 149.3966 at 10iterations 1.448786 54.76011 at 20iterations 0.6425289 25.18342 at 30iterations 0.2852604 11.47296 at 40iterations 0.1264639 4.400789 at 50iterations 5.5914253E-02 2.133442 at 60iterations 2.4802363E-02 1.036402 at 70iterations 1.0948449E-02 0.4371262 at 80iterations 4.8604114E-03 0.1799910 at 90iterations 2.1630733E-03 7.8021765E-02 at 100iterations 9.5717510E-04 3.3920288E-02 at 110iterations 4.2441953E-04 1.6798973E-02 at 120iterations finished qdiffx linear iterations at : 11:02:48 total time elapsed so far: 17.77000 # loops : 120 mean,max change (kT/e) : 4.2441953E-04 1.6798973E-02 energy calculations done at 17.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.94000 DelPhi exited at 11:02:49 17.942u 0.760s 0:19.74 94.7% 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 Dec 28 2011 at 11:02:49 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.728248 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): 1.924000 44.61600 ymin,ymax (A): -24.24600 24.44600 zmin,zma (A): -28.91100 29.80800 x,y,z range (A): 42.69200 48.69200 58.71900 scale (grids/A): 2.728248 object centre (A): 23.27000 9.9999428E-02 0.4485006 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 290.6260 centred at (gu) : 90.51875 89.69869 88.80251 assigned negative charge : -288.6263 centred at (gu) : 91.42226 89.69106 88.73826 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 123034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17202 grid for indexing accessible points = 1.400000 m= 62718 mr = 88905 m= 21750 mr = 52147 m= 4057 mr = 17815 m= 353 mr = 2936 m= 5 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 49951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 14654 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) : 1.818832 object centre at (A) : 23.27000 9.9999428E-02 0.4485006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1066659 0.1325690 midg,1,midg; midg,igrid,midg -5.3015362E-02 -5.0023999E-02 1,midg,midg; igrid,midg,midg 6.2434275E-02 -0.1871141 gauss-seidel spectral radius is 0.9991829 estimated iterations to convergence 276 setup time was (sec) 1.930000 now iterating at: 11:02:52 rms-change max change #iterations 7.813607 269.5631 at 10iterations 4.395216 110.9693 at 20iterations 2.464098 56.67683 at 30iterations 1.376008 30.34609 at 40iterations 0.7664312 16.89718 at 50iterations 0.4267028 9.455526 at 60iterations 0.2373354 5.066930 at 70iterations 0.1321330 3.014771 at 80iterations 7.3609278E-02 1.630779 at 90iterations 4.0956039E-02 0.9228077 at 100iterations 2.2867313E-02 0.4938202 at 110iterations 1.2716033E-02 0.2642851 at 120iterations 7.0713232E-03 0.1514155 at 130iterations 3.9399923E-03 7.7600002E-02 at 140iterations 2.1952291E-03 4.5540810E-02 at 150iterations 1.2224403E-03 2.4948120E-02 at 160iterations 6.8058795E-04 1.4611006E-02 at 170iterations 3.8011788E-04 9.2086792E-03 at 180iterations finished qdiffx linear iterations at : 11:03:20 total time elapsed so far: 30.04000 # loops : 180 mean,max change (kT/e) : 3.8011788E-04 9.2086792E-03 energy calculations done at 30.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.20000 DelPhi exited at 11:03:21 30.206u 0.910s 0:31.77 97.9% 0+0k 0+0io 0pf+0w