Sun Oct 9 14:36:42 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 14:36:43 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1365 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: 0.9086037 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): -1.641000 37.54000 ymin,ymax (A): -13.88400 21.09300 zmin,zma (A): -14.33100 23.20400 x,y,z range (A): 39.18100 34.97700 37.53500 scale (grids/A): 0.9086037 object centre (A): 17.94950 3.604500 4.436501 number of atom coordinates read : 1365 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 204.3293 centred at (gu) : 89.81553 90.37383 90.77421 assigned negative charge : -204.8291 centred at (gu) : 89.45988 90.32634 90.92616 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7971 nv = 96 ne = 84 npr = 28708 no. pairs analyzed = 28708 no. exposed pairs = 1667 no. arc points = 12208 no. surface atoms = 560 nbur = 805 mkacc time = 5.9999987E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 844 mr = 4661 m= 9 mr = 266 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 666 ## 48 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6758 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2907099E-06 -2.0336413E-06 midg,1,midg; midg,igrid,midg -6.2033644E-07 3.8359076E-07 1,midg,midg; igrid,midg,midg -4.1933426E-06 3.4548541E-06 gauss-seidel spectral radius is 0.9935948 estimated iterations to convergence 101 setup time was (sec) 0.4800000 now iterating at: 14:36:43 rms-change max change #iterations 0.4217324 69.29684 at 10iterations 8.0809511E-02 10.05268 at 20iterations 1.5821641E-02 1.806911 at 30iterations 3.0284468E-03 0.4190483 at 40iterations 5.8726006E-04 7.6538086E-02 at 50iterations finished qdiffx linear iterations at : 14:36:46 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 5.8726006E-04 7.6538086E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:36:46 3.112u 0.130s 0:03.54 91.5% 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 Sun Oct 9 2011 at 14:36:46 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1365 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: 2.725811 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): -1.641000 37.54000 ymin,ymax (A): -13.88400 21.09300 zmin,zma (A): -14.33100 23.20400 x,y,z range (A): 39.18100 34.97700 37.53500 scale (grids/A): 2.725811 object centre (A): 17.94950 3.604500 4.436501 number of atom coordinates read : 1365 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 204.3293 centred at (gu) : 89.44682 91.12186 92.32292 assigned negative charge : -204.8291 centred at (gu) : 88.37976 90.97921 92.77852 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12208 grid for indexing accessible points = 1.400000 m= 37873 mr = 57096 m= 11862 mr = 30258 m= 2320 mr = 8891 m= 220 mr = 1510 m= 5 mr = 134 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 0.6600000 number of dielectric boundary points 35766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 10021 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) : 0.9086037 object centre at (A) : 17.94950 3.604500 4.436501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6713853E-02 2.1985849E-02 midg,1,midg; midg,igrid,midg -6.5673783E-02 -8.7748893E-02 1,midg,midg; igrid,midg,midg -2.6024482E-03 0.1135316 gauss-seidel spectral radius is 0.9991462 estimated iterations to convergence 270 setup time was (sec) 0.9100000 now iterating at: 14:36:47 rms-change max change #iterations 5.539380 247.6002 at 10iterations 3.063995 96.87273 at 20iterations 1.678893 48.14969 at 30iterations 0.9227281 25.67188 at 40iterations 0.5076018 13.54868 at 50iterations 0.2789324 7.422546 at 60iterations 0.1529720 3.739826 at 70iterations 8.4042609E-02 2.126746 at 80iterations 4.6097212E-02 1.249269 at 90iterations 2.5293978E-02 0.6359749 at 100iterations 1.3843089E-02 0.3749771 at 110iterations 7.6090554E-03 0.1896133 at 120iterations finished qdiffx linear iterations at : 14:36:53 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 7.6090554E-03 0.1896133 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 14:36:54 7.267u 0.171s 0:07.72 96.2% 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 14:36:54 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1365 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: 4.088717 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): -1.641000 37.54000 ymin,ymax (A): -13.88400 21.09300 zmin,zma (A): -14.33100 23.20400 x,y,z range (A): 39.18100 34.97700 37.53500 scale (grids/A): 4.088717 object centre (A): 17.94950 3.604500 4.436501 number of atom coordinates read : 1365 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 204.3293 centred at (gu) : 89.17027 91.68290 93.48439 assigned negative charge : -204.8291 centred at (gu) : 87.56963 91.46881 94.16787 start vw surface at 0.1100000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 186411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12208 grid for indexing accessible points = 1.400000 m= 108060 mr = 136036 m= 57076 mr = 92144 m= 24354 mr = 49393 m= 8181 mr = 20073 m= 2074 mr = 6483 m= 387 mr = 1584 m= 32 mr = 270 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 80579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 10024 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) : 2.725811 object centre at (A) : 17.94950 3.604500 4.436501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4654334 0.2507358 midg,1,midg; midg,igrid,midg -0.3851226 -0.7053741 1,midg,midg; igrid,midg,midg 0.5601500 0.4879607 gauss-seidel spectral radius is 0.9993492 estimated iterations to convergence 309 setup time was (sec) 2.330000 now iterating at: 14:36:56 rms-change max change #iterations 11.08567 225.1906 at 10iterations 6.562171 123.0006 at 20iterations 3.907117 74.37315 at 30iterations 2.324926 36.03833 at 40iterations 1.378062 21.21996 at 50iterations 0.8193671 12.51898 at 60iterations 0.4876336 7.122242 at 70iterations 0.2897639 4.894454 at 80iterations 0.1722168 2.714261 at 90iterations 0.1021021 1.462557 at 100iterations 6.0861159E-02 0.8743305 at 110iterations 3.6269240E-02 0.5432434 at 120iterations 2.1598971E-02 0.3321629 at 130iterations 1.2902590E-02 0.2101650 at 140iterations 7.7588381E-03 0.1190014 at 150iterations 4.6705212E-03 8.0322266E-02 at 160iterations 2.8430182E-03 5.0121307E-02 at 170iterations 1.7572826E-03 3.0014038E-02 at 180iterations finished qdiffx linear iterations at : 14:37:06 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 1.7572826E-03 3.0014038E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:37:06 11.798u 0.151s 0:12.22 97.7% 0+0k 0+0io 0pf+0w