Wed Feb 15 08:55:40 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 08:55:40 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 = 2550 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: 0.6095995 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): -21.36600 37.03300 ymin,ymax (A): -24.00900 26.67100 zmin,zma (A): -10.02800 38.69900 x,y,z range (A): 58.39900 50.68000 48.72700 scale (grids/A): 0.6095995 object centre (A): 7.833501 1.331000 14.33550 number of atom coordinates read : 2550 total number of charged atoms : 2407 net assigned charge : -0.4999919 assigned positive charge : 382.9647 centred at (gu) : 91.43617 89.72993 89.71912 assigned negative charge : -383.4655 centred at (gu) : 91.35462 89.82690 89.75637 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6455 nv = 96 ne = 84 npr = 49899 no. pairs analyzed = 49899 no. exposed pairs = 3561 no. arc points = 25541 no. surface atoms = 1183 nbur = 1367 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3147 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2511 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5147209E-09 -2.0408804E-09 midg,1,midg; midg,igrid,midg 4.5285171E-09 -4.7967963E-09 1,midg,midg; igrid,midg,midg -3.1405134E-09 4.9152105E-09 gauss-seidel spectral radius is 0.9860769 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 08:55:41 rms-change max change #iterations 0.1097534 18.29776 at 10iterations 9.6414052E-03 1.424076 at 20iterations 8.4031495E-04 0.1192999 at 30iterations 7.4999021E-05 1.2050629E-02 at 40iterations 7.0123788E-06 1.0318756E-03 at 50iterations finished qdiffx linear iterations at : 08:55:43 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.0123788E-06 1.0318756E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 08:55:44 3.445u 0.150s 0:04.38 81.9% 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 08:55:44 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 = 2550 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: 1.828798 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): -21.36600 37.03300 ymin,ymax (A): -24.00900 26.67100 zmin,zma (A): -10.02800 38.69900 x,y,z range (A): 58.39900 50.68000 48.72700 scale (grids/A): 1.828798 object centre (A): 7.833501 1.331000 14.33550 number of atom coordinates read : 2550 total number of charged atoms : 2407 net assigned charge : -0.4999919 assigned positive charge : 382.9647 centred at (gu) : 94.30791 89.18919 89.15676 assigned negative charge : -383.4655 centred at (gu) : 94.06351 89.48058 89.26881 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25541 grid for indexing accessible points = 1.400000 m= 22836 mr = 45350 m= 3085 mr = 15427 m= 187 mr = 1620 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 33386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18814 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) : 0.6095995 object centre at (A) : 7.833501 1.331000 14.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2462913E-02 -1.6488214E-03 midg,1,midg; midg,igrid,midg 3.3920559E-03 -1.8622790E-02 1,midg,midg; igrid,midg,midg -3.3682551E-02 2.5027724E-02 gauss-seidel spectral radius is 0.9985335 estimated iterations to convergence 207 setup time was (sec) 0.8300000 now iterating at: 08:55:46 rms-change max change #iterations 3.874006 174.7109 at 10iterations 1.751833 75.36385 at 20iterations 0.7962560 30.10187 at 30iterations 0.3594096 12.90705 at 40iterations 0.1639931 5.901696 at 50iterations 7.4313015E-02 2.514736 at 60iterations 3.3746969E-02 1.309385 at 70iterations 1.5307441E-02 0.5781975 at 80iterations 6.9594393E-03 0.2482204 at 90iterations 3.1546946E-03 0.1052680 at 100iterations 1.4399929E-03 4.9468815E-02 at 110iterations 6.5589027E-04 2.1842957E-02 at 120iterations finished qdiffx linear iterations at : 08:55:52 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 6.5589027E-04 2.1842957E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 08:55:53 7.872u 0.195s 0:08.57 94.0% 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 Feb 15 2012 at 08:55:53 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 = 2550 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: 2.743197 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): -21.36600 37.03300 ymin,ymax (A): -24.00900 26.67100 zmin,zma (A): -10.02800 38.69900 x,y,z range (A): 58.39900 50.68000 48.72700 scale (grids/A): 2.743197 object centre (A): 7.833501 1.331000 14.33550 number of atom coordinates read : 2550 total number of charged atoms : 2407 net assigned charge : -0.4999919 assigned positive charge : 382.9647 centred at (gu) : 96.46179 88.78350 88.73495 assigned negative charge : -383.4655 centred at (gu) : 96.09529 89.22079 88.90322 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25541 grid for indexing accessible points = 1.400000 m= 75308 mr = 111107 m= 24447 mr = 58785 m= 5049 mr = 18063 m= 710 mr = 3381 m= 48 mr = 402 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 75238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 19255 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) : 1.828798 object centre at (A) : 7.833501 1.331000 14.33550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1869793 2.0070588E-02 midg,1,midg; midg,igrid,midg 7.1503446E-02 -0.2812290 1,midg,midg; igrid,midg,midg -0.3553146 0.4738296 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 1.710000 now iterating at: 08:55:55 rms-change max change #iterations 9.606760 362.8835 at 10iterations 5.715364 135.7215 at 20iterations 3.344932 86.92560 at 30iterations 1.943720 47.96059 at 40iterations 1.125187 25.08164 at 50iterations 0.6486322 12.89122 at 60iterations 0.3728392 9.025790 at 70iterations 0.2141482 4.191272 at 80iterations 0.1226032 2.506780 at 90iterations 7.0221633E-02 1.347641 at 100iterations 4.0126845E-02 0.8493462 at 110iterations 2.2950778E-02 0.4283218 at 120iterations 1.3140536E-02 0.2576714 at 130iterations 7.5131417E-03 0.1518669 at 140iterations 4.2900424E-03 8.3564758E-02 at 150iterations 2.4472829E-03 5.0621033E-02 at 160iterations 1.4004707E-03 2.7013183E-02 at 170iterations 7.9886970E-04 1.4559746E-02 at 180iterations finished qdiffx linear iterations at : 08:56:06 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 7.9886970E-04 1.4559746E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 08:56:07 12.992u 0.315s 0:13.86 95.9% 0+0k 0+0io 0pf+0w