Wed Dec 28 11:04:22 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+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 Wed Dec 28 2011 at 11:04:22 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 = 1964 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: 0.6086094 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 0.6086094 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.28234 90.37507 89.54966 assigned negative charge : -285.8263 centred at (gu) : 90.28715 90.49657 89.38713 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4895 nv = 96 ne = 84 npr = 40054 no. pairs analyzed = 40054 no. exposed pairs = 2481 no. arc points = 17575 no. surface atoms = 840 nbur = 1124 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 217 mr = 2649 m= 0 mr = 9 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2700000 number of dielectric boundary points 2454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1897 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1108668E-09 6.1091017E-09 midg,1,midg; midg,igrid,midg 4.9386815E-09 -3.4075651E-09 1,midg,midg; igrid,midg,midg 1.2721277E-09 1.0807139E-09 gauss-seidel spectral radius is 0.9859703 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 11:04:23 rms-change max change #iterations 9.7056441E-02 16.95622 at 10iterations 8.5075768E-03 1.597836 at 20iterations 7.3909730E-04 0.1252937 at 30iterations 6.3813146E-05 1.3930321E-02 at 40iterations 5.6215845E-06 9.6511841E-04 at 50iterations finished qdiffx linear iterations at : 11:04:26 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 5.6215845E-06 9.6511841E-04 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 11:04:27 4.391u 0.237s 0:04.97 92.9% 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 Dec 28 2011 at 11:04:27 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 = 1964 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: 1.825828 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 1.825828 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.84687 91.12537 88.64951 assigned negative charge : -285.8263 centred at (gu) : 90.86170 91.48988 88.16155 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 53253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17575 grid for indexing accessible points = 1.400000 m= 18208 mr = 36345 m= 2226 mr = 13499 m= 67 mr = 1315 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1133 time to turn everything in is 0.4000000 number of dielectric boundary points 22586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14343 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) : 0.6086094 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9396808E-03 1.0987080E-02 midg,1,midg; midg,igrid,midg 5.4465178E-03 -5.5583939E-03 1,midg,midg; igrid,midg,midg 3.2129403E-02 3.0479835E-02 gauss-seidel spectral radius is 0.9984394 estimated iterations to convergence 201 setup time was (sec) 0.6700000 now iterating at: 11:04:28 rms-change max change #iterations 3.280626 165.1740 at 10iterations 1.452870 59.99630 at 20iterations 0.6433423 24.59275 at 30iterations 0.2863091 10.12551 at 40iterations 0.1272262 4.702679 at 50iterations 5.6653548E-02 2.083984 at 60iterations 2.5009470E-02 0.8876419 at 70iterations 1.1125754E-02 0.4116935 at 80iterations 4.9299202E-03 0.1750684 at 90iterations 2.2018931E-03 7.7945709E-02 at 100iterations 9.7551360E-04 3.5709381E-02 at 110iterations 4.3267210E-04 1.7304182E-02 at 120iterations finished qdiffx linear iterations at : 11:04:34 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 4.3267210E-04 1.7304182E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 11:04:35 6.959u 0.197s 0:07.84 91.0% 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 Dec 28 2011 at 11:04:35 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 = 1964 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: 2.738742 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 2.738742 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.27039 91.68803 87.97433 assigned negative charge : -285.8263 centred at (gu) : 91.29253 92.23484 87.24246 start vw surface at 0.1300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 123189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17575 grid for indexing accessible points = 1.400000 m= 60516 mr = 88056 m= 19877 mr = 49757 m= 3727 mr = 15999 m= 328 mr = 2709 m= 7 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 3746 time to turn everything in is 0.9300000 number of dielectric boundary points 50953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 14655 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) : 1.825828 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1377065E-02 9.6868910E-02 midg,1,midg; midg,igrid,midg 3.4343436E-02 -5.2199744E-02 1,midg,midg; igrid,midg,midg 0.3592618 0.3320616 gauss-seidel spectral radius is 0.9991875 estimated iterations to convergence 277 setup time was (sec) 1.250000 now iterating at: 11:04:36 rms-change max change #iterations 7.867159 343.1906 at 10iterations 4.450829 119.4731 at 20iterations 2.504172 56.96574 at 30iterations 1.398306 31.18463 at 40iterations 0.7835283 18.00702 at 50iterations 0.4369822 9.992123 at 60iterations 0.2439767 5.306473 at 70iterations 0.1361697 3.098125 at 80iterations 7.6229185E-02 1.676431 at 90iterations 4.2481292E-02 0.9118984 at 100iterations 2.3630729E-02 0.5195713 at 110iterations 1.3213453E-02 0.2745152 at 120iterations 7.3653669E-03 0.1460762 at 130iterations 4.1151685E-03 8.6117744E-02 at 140iterations 2.3002792E-03 4.9540401E-02 at 150iterations 1.2796242E-03 2.7652740E-02 at 160iterations 7.1309623E-04 1.7443359E-02 at 170iterations 3.9777992E-04 8.5868835E-03 at 180iterations finished qdiffx linear iterations at : 11:04:47 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 3.9777992E-04 8.5868835E-03 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 11:04:47 11.686u 0.313s 0:12.55 95.5% 0+0k 0+0io 0pf+0w