Wed Feb 15 08:56:21 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:21 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: GLU 696 has a net charge of -2.0000 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: 0.6003778 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 0.6003778 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.000013 assigned positive charge : 378.4471 centred at (gu) : 90.59590 90.31767 90.87253 assigned negative charge : -376.4481 centred at (gu) : 90.58933 90.28594 90.89098 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6057 nv = 96 ne = 84 npr = 52378 no. pairs analyzed = 52378 no. exposed pairs = 3387 no. arc points = 23924 no. surface atoms = 1134 nbur = 1427 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3054 m= 0 mr = 26 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2422 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2562588E-09 2.4076502E-10 midg,1,midg; midg,igrid,midg -2.4979324E-10 2.1475233E-09 1,midg,midg; igrid,midg,midg 5.5632660E-10 1.2587166E-09 gauss-seidel spectral radius is 0.9856419 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 08:56:22 rms-change max change #iterations 0.1019818 18.92067 at 10iterations 8.7328665E-03 1.452076 at 20iterations 7.4640784E-04 0.1101513 at 30iterations 6.8647321E-05 1.0890961E-02 at 40iterations 9.1759821E-06 1.3604164E-03 at 50iterations finished qdiffx linear iterations at : 08:56:25 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 9.1759821E-06 1.3604164E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:56:25 3.332u 0.146s 0:03.83 90.6% 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 Feb 15 2012 at 08:56:25 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: GLU 696 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.801133 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 1.801133 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.000013 assigned positive charge : 378.4471 centred at (gu) : 91.78725 90.95252 92.61722 assigned negative charge : -376.4481 centred at (gu) : 91.76785 90.85782 92.67297 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23924 grid for indexing accessible points = 1.400000 m= 22095 mr = 43913 m= 3232 mr = 15356 m= 165 mr = 1820 m= 1 mr = 39 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 0.5300000 number of dielectric boundary points 30314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18990 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) : 0.6003778 object centre at (A) : 11.36350 33.37500 21.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4011123E-02 -2.0279851E-02 midg,1,midg; midg,igrid,midg -2.0000464E-03 8.6182794E-03 1,midg,midg; igrid,midg,midg 2.5532499E-03 -5.2239480E-03 gauss-seidel spectral radius is 0.9984801 estimated iterations to convergence 203 setup time was (sec) 0.8500000 now iterating at: 08:56:26 rms-change max change #iterations 3.723401 175.4020 at 10iterations 1.661069 64.78004 at 20iterations 0.7479549 27.94261 at 30iterations 0.3357078 10.97707 at 40iterations 0.1510354 5.131259 at 50iterations 6.7882113E-02 2.230598 at 60iterations 3.0476581E-02 1.099955 at 70iterations 1.3652215E-02 0.4562845 at 80iterations 6.1547998E-03 0.2350464 at 90iterations 2.7658520E-03 9.8236084E-02 at 100iterations 1.2425815E-03 4.1835785E-02 at 110iterations 5.6181650E-04 1.8880844E-02 at 120iterations finished qdiffx linear iterations at : 08:56:33 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 5.6181650E-04 1.8880844E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 08:56:34 7.957u 0.264s 0:08.56 95.9% 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 Wed Feb 15 2012 at 08:56:34 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: GLU 696 has a net charge of -2.0000 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: 2.701700 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 2.701700 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.000013 assigned positive charge : 378.4471 centred at (gu) : 92.68078 91.42876 93.92571 assigned negative charge : -376.4481 centred at (gu) : 92.65176 91.28690 94.00951 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 152986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23924 grid for indexing accessible points = 1.400000 m= 72156 mr = 107567 m= 24745 mr = 56822 m= 5472 mr = 18983 m= 633 mr = 3856 m= 32 mr = 368 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 68426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19395 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) : 1.801133 object centre at (A) : 11.36350 33.37500 21.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3234459 -0.1628546 midg,1,midg; midg,igrid,midg -0.1014866 3.8093042E-02 1,midg,midg; igrid,midg,midg 1.0645672E-02 -8.3593778E-02 gauss-seidel spectral radius is 0.9992232 estimated iterations to convergence 283 setup time was (sec) 1.560000 now iterating at: 08:56:36 rms-change max change #iterations 9.191636 321.0598 at 10iterations 5.367865 137.4135 at 20iterations 3.093975 66.65143 at 30iterations 1.776685 38.55959 at 40iterations 1.025117 21.17931 at 50iterations 0.5848993 13.95379 at 60iterations 0.3343063 7.742610 at 70iterations 0.1903267 4.242733 at 80iterations 0.1085649 2.191662 at 90iterations 6.1846085E-02 1.237598 at 100iterations 3.5143036E-02 0.7073936 at 110iterations 2.0004764E-02 0.4264898 at 120iterations 1.1383606E-02 0.2392654 at 130iterations 6.4806184E-03 0.1442413 at 140iterations 3.6892483E-03 7.7468395E-02 at 150iterations 2.1050195E-03 4.2845726E-02 at 160iterations 1.2056355E-03 2.5226593E-02 at 170iterations 6.9617183E-04 1.3927460E-02 at 180iterations finished qdiffx linear iterations at : 08:56:48 total time elapsed so far: 14.15000 # loops : 180 mean,max change (kT/e) : 6.9617183E-04 1.3927460E-02 energy calculations done at 14.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.35000 DelPhi exited at 08:56:49 14.351u 0.252s 0:15.08 96.8% 0+0k 0+0io 0pf+0w