Sun Oct 9 15:40:51 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 15:40:51 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5672 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5016699 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): 67.35700 138.3200 ymin,ymax (A): -6.168000 57.04100 zmin,zma (A): -3.345000 66.68100 x,y,z range (A): 70.96299 63.20900 70.02600 scale (grids/A): 0.5016699 object centre (A): 102.8385 25.43650 31.66800 number of atom coordinates read : 5672 total number of charged atoms : 5501 net assigned charge : -2.471966 assigned positive charge : 869.2452 centred at (gu) : 89.81374 90.83712 89.95328 assigned negative charge : -871.7250 centred at (gu) : 89.87392 90.77427 90.05543 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8621 nv = 96 ne = 84 npr = 117871 no. pairs analyzed = 117871 no. exposed pairs = 6440 no. arc points = 44899 no. surface atoms = 2162 nbur = 3510 mkacc time = 0.2500000 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 = 1.708000 m= 302 mr = 4668 m= 0 mr = 8 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.5000000 number of dielectric boundary points 4247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4315 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11881 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9391252E-10 -2.4423463E-10 midg,1,midg; midg,igrid,midg -1.2855690E-10 1.3722695E-10 1,midg,midg; igrid,midg,midg 1.0871409E-10 -1.4759077E-10 gauss-seidel spectral radius is 0.9797323 estimated iterations to convergence 58 setup time was (sec) 0.7100000 now iterating at: 15:40:52 rms-change max change #iterations 6.8136178E-02 10.23031 at 10iterations 4.3765143E-03 0.5430336 at 20iterations 7.6131156E-04 0.1179962 at 30iterations 2.2949168E-04 3.5983086E-02 at 40iterations 7.2076240E-05 1.1081696E-02 at 50iterations finished qdiffx linear iterations at : 15:40:55 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 7.2076240E-05 1.1081696E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 15:40:55 3.336u 0.148s 0:03.76 92.2% 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 15:40:55 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5672 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.505010 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): 67.35700 138.3200 ymin,ymax (A): -6.168000 57.04100 zmin,zma (A): -3.345000 66.68100 x,y,z range (A): 70.96299 63.20900 70.02600 scale (grids/A): 1.505010 object centre (A): 102.8385 25.43650 31.66800 number of atom coordinates read : 5672 total number of charged atoms : 5501 net assigned charge : -2.471966 assigned positive charge : 869.2452 centred at (gu) : 89.43965 92.50940 89.85796 assigned negative charge : -871.7250 centred at (gu) : 89.62195 92.32272 90.16615 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 99575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44899 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28502 mr = 70456 m= 2394 mr = 19392 m= 47 mr = 1026 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3924 time to turn everything in is 0.6600000 number of dielectric boundary points 39644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 604 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 41041 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) : 0.5016699 object centre at (A) : 102.8385 25.43650 31.66800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3471273E-03 2.9733416E-03 midg,1,midg; midg,igrid,midg -9.0191178E-03 6.0534151E-03 1,midg,midg; igrid,midg,midg -1.7415173E-02 -8.1974538E-03 gauss-seidel spectral radius is 0.9981027 estimated iterations to convergence 182 setup time was (sec) 0.9400000 now iterating at: 15:40:56 rms-change max change #iterations 4.072201 158.6656 at 10iterations 1.664052 54.06377 at 20iterations 0.6811568 22.00225 at 30iterations 0.2797973 9.137481 at 40iterations 0.1144185 3.768980 at 50iterations 4.7060810E-02 1.426304 at 60iterations 1.9366389E-02 0.5491600 at 70iterations 7.9849372E-03 0.2542763 at 80iterations 3.3379127E-03 9.8980904E-02 at 90iterations 1.4208908E-03 5.3324699E-02 at 100iterations 6.3191744E-04 2.1337509E-02 at 110iterations 3.0552602E-04 1.0452271E-02 at 120iterations finished qdiffx linear iterations at : 15:41:02 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 3.0552602E-04 1.0452271E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 15:41:03 7.148u 0.151s 0:07.61 95.7% 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 Sun Oct 9 2011 at 15:41:03 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5672 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.257515 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): 67.35700 138.3200 ymin,ymax (A): -6.168000 57.04100 zmin,zma (A): -3.345000 66.68100 x,y,z range (A): 70.96299 63.20900 70.02600 scale (grids/A): 2.257515 object centre (A): 102.8385 25.43650 31.66800 number of atom coordinates read : 5672 total number of charged atoms : 5501 net assigned charge : -2.471966 assigned positive charge : 869.2452 centred at (gu) : 89.15884 93.76372 89.78661 assigned negative charge : -871.7250 centred at (gu) : 89.43280 93.48396 90.24909 start vw surface at 0.2400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 232745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44899 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 103328 mr = 173036 m= 25864 mr = 81653 m= 3440 mr = 19044 m= 166 mr = 2134 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 12468 time to turn everything in is 1.590000 number of dielectric boundary points 89624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 43867 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) : 1.505010 object centre at (A) : 102.8385 25.43650 31.66800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4947870E-02 0.2062307 midg,1,midg; midg,igrid,midg -0.2060515 0.2010668 1,midg,midg; igrid,midg,midg -0.5331641 0.1447544 gauss-seidel spectral radius is 0.9991701 estimated iterations to convergence 274 setup time was (sec) 1.870000 now iterating at: 15:41:05 rms-change max change #iterations 11.03609 316.7416 at 10iterations 6.299503 156.9859 at 20iterations 3.568714 74.84485 at 30iterations 2.016110 40.24950 at 40iterations 1.134969 22.05748 at 50iterations 0.6375394 14.14995 at 60iterations 0.3569185 7.161472 at 70iterations 0.1996143 3.672411 at 80iterations 0.1118874 1.896118 at 90iterations 6.2336013E-02 1.131900 at 100iterations 3.4769889E-02 0.6307154 at 110iterations 1.9395942E-02 0.3512192 at 120iterations 1.0830126E-02 0.2003822 at 130iterations 6.0394807E-03 0.1077347 at 140iterations 3.3725461E-03 5.8928967E-02 at 150iterations 1.8823787E-03 3.4626484E-02 at 160iterations 1.0535814E-03 1.9071579E-02 at 170iterations 5.9520750E-04 1.0084629E-02 at 180iterations finished qdiffx linear iterations at : 15:41:15 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 5.9520750E-04 1.0084629E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 15:41:15 11.927u 0.185s 0:12.42 97.4% 0+0k 0+0io 0pf+0w