Sat Oct 8 18:12:50 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+sph.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 Sat Oct 8 2011 at 18:12:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 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: 0.5862591 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): 8.776999 65.10000 ymin,ymax (A): -18.91600 41.80800 zmin,zma (A): 7.149000 56.40500 x,y,z range (A): 56.32300 60.72400 49.25600 scale (grids/A): 0.5862591 object centre (A): 36.93850 11.44600 31.77700 number of atom coordinates read : 3153 total number of charged atoms : 3010 net assigned charge : -0.9999948 assigned positive charge : 470.4629 centred at (gu) : 88.80097 90.64185 89.49785 assigned negative charge : -471.4641 centred at (gu) : 88.72866 90.54962 89.53571 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7301 nv = 96 ne = 84 npr = 63631 no. pairs analyzed = 63631 no. exposed pairs = 3861 no. arc points = 26401 no. surface atoms = 1295 nbur = 1858 mkacc time = 0.1700000 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= 359 mr = 4153 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3500000 number of dielectric boundary points 3491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2668 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1732894E-10 -1.2043928E-09 midg,1,midg; midg,igrid,midg -2.5242965E-09 2.7325175E-09 1,midg,midg; igrid,midg,midg -3.1249039E-09 1.3457276E-09 gauss-seidel spectral radius is 0.9849936 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 18:12:52 rms-change max change #iterations 0.1064697 15.80189 at 10iterations 8.6820088E-03 1.249306 at 20iterations 7.1936368E-04 9.6757889E-02 at 30iterations 6.7032939E-05 1.0199547E-02 at 40iterations 9.0657186E-06 1.4467239E-03 at 50iterations finished qdiffx linear iterations at : 18:12:55 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 9.0657186E-06 1.4467239E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 18:12:56 4.545u 0.402s 0:05.21 94.8% 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 8 2011 at 18:12:56 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 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: 1.758777 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): 8.776999 65.10000 ymin,ymax (A): -18.91600 41.80800 zmin,zma (A): 7.149000 56.40500 x,y,z range (A): 56.32300 60.72400 49.25600 scale (grids/A): 1.758777 object centre (A): 36.93850 11.44600 31.77700 number of atom coordinates read : 3153 total number of charged atoms : 3010 net assigned charge : -0.9999948 assigned positive charge : 470.4629 centred at (gu) : 86.40188 91.92463 88.49244 assigned negative charge : -471.4641 centred at (gu) : 86.18584 91.64862 88.60670 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26401 grid for indexing accessible points = 1.400000 m= 29075 mr = 57013 m= 3979 mr = 21436 m= 187 mr = 2331 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 32361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23399 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) : 0.5862591 object centre at (A) : 36.93850 11.44600 31.77700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8417364E-03 -7.1771131E-03 midg,1,midg; midg,igrid,midg -3.3983544E-02 6.1032237E-03 1,midg,midg; igrid,midg,midg 3.1976341E-03 3.0703295E-02 gauss-seidel spectral radius is 0.9984577 estimated iterations to convergence 202 setup time was (sec) 0.9600000 now iterating at: 18:12:57 rms-change max change #iterations 4.031878 157.3782 at 10iterations 1.796924 60.65357 at 20iterations 0.8004552 28.08289 at 30iterations 0.3593521 11.75823 at 40iterations 0.1603222 5.361489 at 50iterations 7.1707748E-02 2.384371 at 60iterations 3.2115895E-02 0.9775162 at 70iterations 1.4372184E-02 0.4773273 at 80iterations 6.4084455E-03 0.1893764 at 90iterations 2.8788673E-03 9.9840164E-02 at 100iterations 1.2902151E-03 4.6845198E-02 at 110iterations 5.8255752E-04 1.7819881E-02 at 120iterations finished qdiffx linear iterations at : 18:13:07 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 5.8255752E-04 1.7819881E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.73000 DelPhi exited at 18:13:07 10.734u 0.466s 0:11.47 97.5% 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 8 2011 at 18:13:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 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: 2.638166 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): 8.776999 65.10000 ymin,ymax (A): -18.91600 41.80800 zmin,zma (A): 7.149000 56.40500 x,y,z range (A): 56.32300 60.72400 49.25600 scale (grids/A): 2.638166 object centre (A): 36.93850 11.44600 31.77700 number of atom coordinates read : 3153 total number of charged atoms : 3010 net assigned charge : -0.9999948 assigned positive charge : 470.4629 centred at (gu) : 84.60272 92.88667 87.73849 assigned negative charge : -471.4641 centred at (gu) : 84.27858 92.47281 87.90998 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26401 grid for indexing accessible points = 1.400000 m= 96179 mr = 138187 m= 32282 mr = 79189 m= 6760 mr = 25631 m= 793 mr = 4926 m= 21 mr = 449 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 72991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 24069 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) : 1.758777 object centre at (A) : 36.93850 11.44600 31.77700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1527868 -8.1272453E-02 midg,1,midg; midg,igrid,midg -0.4772555 0.1409099 1,midg,midg; igrid,midg,midg -3.4258168E-02 0.3688704 gauss-seidel spectral radius is 0.9992221 estimated iterations to convergence 283 setup time was (sec) 2.080000 now iterating at: 18:13:10 rms-change max change #iterations 9.826356 290.4513 at 10iterations 5.688587 135.8008 at 20iterations 3.261201 67.22031 at 30iterations 1.864223 35.76232 at 40iterations 1.066535 20.02649 at 50iterations 0.6082799 11.21084 at 60iterations 0.3461312 6.418682 at 70iterations 0.1969755 3.629175 at 80iterations 0.1118690 2.082869 at 90iterations 6.3610442E-02 1.112297 at 100iterations 3.6100607E-02 0.6462612 at 110iterations 2.0482175E-02 0.4164467 at 120iterations 1.1640848E-02 0.2011821 at 130iterations 6.6254055E-03 0.1202126 at 140iterations 3.7739372E-03 6.7306519E-02 at 150iterations 2.1582509E-03 3.6639214E-02 at 160iterations 1.2421446E-03 2.3401737E-02 at 170iterations 7.2372652E-04 1.3916016E-02 at 180iterations finished qdiffx linear iterations at : 18:13:26 total time elapsed so far: 18.04000 # loops : 180 mean,max change (kT/e) : 7.2372652E-04 1.3916016E-02 energy calculations done at 18.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.20000 DelPhi exited at 18:13:26 18.207u 0.463s 0:19.16 97.3% 0+0k 0+0io 0pf+0w