Tue Nov 22 14:11:33 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 Tue Nov 22 2011 at 14:11:38 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5525376 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): -35.35300 11.72500 ymin,ymax (A): 0.4230000 42.76200 zmin,zma (A): -3.419000 61.01100 x,y,z range (A): 47.07800 42.33900 64.43000 scale (grids/A): 0.5525376 object centre (A): -11.81400 21.59250 28.79600 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 294.1999 centred at (gu) : 90.06419 89.29462 89.44254 assigned negative charge : -291.2002 centred at (gu) : 89.98663 89.41489 89.44194 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 3983 nv = 96 ne = 84 npr = 40375 no. pairs analyzed = 40375 no. exposed pairs = 2456 no. arc points = 17327 no. surface atoms = 833 nbur = 1137 mkacc time = 9.0000004E-02 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 = 1.568000 m= 149 mr = 2098 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6529831E-10 2.0952773E-10 midg,1,midg; midg,igrid,midg 1.0629494E-09 -3.6893671E-10 1,midg,midg; igrid,midg,midg -1.9539585E-10 6.7234462E-10 gauss-seidel spectral radius is 0.9830282 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 14:11:40 rms-change max change #iterations 6.2919065E-02 13.36627 at 10iterations 4.3008253E-03 0.8305578 at 20iterations 2.9504718E-04 5.9112549E-02 at 30iterations 2.0181466E-05 3.6888123E-03 at 40iterations 1.3969976E-06 2.7823448E-04 at 50iterations finished qdiffx linear iterations at : 14:11:45 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.3969976E-06 2.7823448E-04 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 14:11:46 3.260u 0.202s 0:09.30 37.2% 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 Tue Nov 22 2011 at 14:11:49 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.657613 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): -35.35300 11.72500 ymin,ymax (A): 0.4230000 42.76200 zmin,zma (A): -3.419000 61.01100 x,y,z range (A): 47.07800 42.33900 64.43000 scale (grids/A): 1.657613 object centre (A): -11.81400 21.59250 28.79600 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 294.1999 centred at (gu) : 90.19243 87.88362 88.32742 assigned negative charge : -291.2002 centred at (gu) : 89.95998 88.24478 88.32602 start vw surface at 0.1200000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 43478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17327 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14026 mr = 29224 m= 1507 mr = 10157 m= 37 mr = 821 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 452 time to turn everything in is 0.3400000 number of dielectric boundary points 18846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14149 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) : 0.5525376 object centre at (A) : -11.81400 21.59250 28.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9364513E-02 1.3976018E-02 midg,1,midg; midg,igrid,midg 1.2693937E-03 -3.5672062E-03 1,midg,midg; igrid,midg,midg -1.3196155E-03 5.5019156E-04 gauss-seidel spectral radius is 0.9981166 estimated iterations to convergence 183 setup time was (sec) 0.6100000 now iterating at: 14:11:50 rms-change max change #iterations 2.760548 158.8014 at 10iterations 1.126284 50.76811 at 20iterations 0.4635207 20.39969 at 30iterations 0.1899868 8.037219 at 40iterations 7.7990308E-02 3.462547 at 50iterations 3.1848378E-02 1.510899 at 60iterations 1.2976912E-02 0.5946198 at 70iterations 5.3406833E-03 0.2251070 at 80iterations 2.2004242E-03 0.1003208 at 90iterations 9.0324931E-04 3.6497116E-02 at 100iterations 3.7075172E-04 1.6557693E-02 at 110iterations 1.5204286E-04 7.0304871E-03 at 120iterations finished qdiffx linear iterations at : 14:12:10 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.5204286E-04 7.0304871E-03 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 14:12:12 7.461u 0.206s 0:23.11 33.1% 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 Tue Nov 22 2011 at 14:12:14 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.486419 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): -35.35300 11.72500 ymin,ymax (A): 0.4230000 42.76200 zmin,zma (A): -3.419000 61.01100 x,y,z range (A): 47.07800 42.33900 64.43000 scale (grids/A): 2.486419 object centre (A): -11.81400 21.59250 28.79600 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 294.1999 centred at (gu) : 90.28873 86.82542 87.49110 assigned negative charge : -291.2002 centred at (gu) : 89.93999 87.36718 87.48913 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 100746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17327 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 47909 mr = 71235 m= 14558 mr = 38779 m= 2501 mr = 11599 m= 148 mr = 1690 m= 4 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1524 time to turn everything in is 0.7500000 number of dielectric boundary points 42492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14694 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) : 1.657613 object centre at (A) : -11.81400 21.59250 28.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2067249 0.1295118 midg,1,midg; midg,igrid,midg -1.2820885E-02 -6.4185441E-02 1,midg,midg; igrid,midg,midg -3.2275435E-02 -1.5148023E-02 gauss-seidel spectral radius is 0.9990792 estimated iterations to convergence 260 setup time was (sec) 1.040000 now iterating at: 14:12:17 rms-change max change #iterations 7.004358 299.7120 at 10iterations 3.814614 119.8121 at 20iterations 2.067082 52.69600 at 30iterations 1.113664 28.36893 at 40iterations 0.6017014 15.40240 at 50iterations 0.3245308 7.630091 at 60iterations 0.1750180 4.592064 at 70iterations 9.3872309E-02 2.411568 at 80iterations 5.0584491E-02 1.276472 at 90iterations 2.7194967E-02 0.6413870 at 100iterations 1.4612910E-02 0.3667564 at 110iterations 7.8549217E-03 0.2130585 at 120iterations 4.2206408E-03 0.1188664 at 130iterations 2.2744366E-03 5.4212570E-02 at 140iterations 1.2201314E-03 3.3630371E-02 at 150iterations 6.5690657E-04 1.5739441E-02 at 160iterations 3.5157808E-04 9.9506378E-03 at 170iterations 1.8923188E-04 4.3907166E-03 at 180iterations finished qdiffx linear iterations at : 14:12:38 total time elapsed so far: 10.78000 # loops : 180 mean,max change (kT/e) : 1.8923188E-04 4.3907166E-03 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 14:12:39 10.950u 0.235s 0:25.82 43.2% 0+0k 0+0io 0pf+0w