Tue Oct 11 03:40:30 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+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 Tue Oct 11 2011 at 03:40:30 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 = 2649 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: 0.6635478 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): -14.85600 33.84000 ymin,ymax (A): 7.072999 55.57000 zmin,zma (A): 25.94700 79.59800 x,y,z range (A): 48.69600 48.49700 53.65100 scale (grids/A): 0.6635478 object centre (A): 9.492001 31.32150 52.77250 number of atom coordinates read : 2649 total number of charged atoms : 2501 net assigned charge : 2.500012 assigned positive charge : 400.5259 centred at (gu) : 89.95461 90.20067 88.52557 assigned negative charge : -398.0264 centred at (gu) : 90.18266 90.01063 88.58160 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 53837 no. pairs analyzed = 53837 no. exposed pairs = 3181 no. arc points = 22341 no. surface atoms = 1073 nbur = 1576 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4562 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3600000 number of dielectric boundary points 3736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2151 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6014199E-08 -4.1216346E-09 midg,1,midg; midg,igrid,midg -3.4712293E-08 5.0133842E-08 1,midg,midg; igrid,midg,midg 5.6670189E-08 -4.4610374E-08 gauss-seidel spectral radius is 0.9882302 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 03:40:31 rms-change max change #iterations 0.1706867 21.34244 at 10iterations 1.8818324E-02 2.457420 at 20iterations 2.1100123E-03 0.2638931 at 30iterations 2.5971720E-04 3.6586761E-02 at 40iterations 4.7197638E-05 6.2561035E-03 at 50iterations finished qdiffx linear iterations at : 03:40:34 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 4.7197638E-05 6.2561035E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 03:40:35 4.068u 0.282s 0:05.33 81.4% 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 Oct 11 2011 at 03:40:35 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 = 2649 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: 1.990643 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): -14.85600 33.84000 ymin,ymax (A): 7.072999 55.57000 zmin,zma (A): 25.94700 79.59800 x,y,z range (A): 48.69600 48.49700 53.65100 scale (grids/A): 1.990643 object centre (A): 9.492001 31.32150 52.77250 number of atom coordinates read : 2649 total number of charged atoms : 2501 net assigned charge : 2.500012 assigned positive charge : 400.5259 centred at (gu) : 89.86311 90.60146 85.57605 assigned negative charge : -398.0264 centred at (gu) : 90.54786 90.03152 85.74432 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22341 grid for indexing accessible points = 1.400000 m= 32464 mr = 60585 m= 5586 mr = 24568 m= 428 mr = 3761 m= 12 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1375 time to turn everything in is 0.7500000 number of dielectric boundary points 34398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 19731 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) : 0.6635478 object centre at (A) : 9.492001 31.32150 52.77250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3798075E-03 -3.0066514E-02 midg,1,midg; midg,igrid,midg -1.8181529E-02 4.8716966E-02 1,midg,midg; igrid,midg,midg 6.4551555E-02 -1.4681434E-02 gauss-seidel spectral radius is 0.9987512 estimated iterations to convergence 224 setup time was (sec) 1.050000 now iterating at: 03:40:37 rms-change max change #iterations 4.706530 217.3678 at 10iterations 2.289192 68.96178 at 20iterations 1.106677 33.69427 at 30iterations 0.5396334 19.03489 at 40iterations 0.2608092 7.543223 at 50iterations 0.1268776 3.868198 at 60iterations 6.1351940E-02 1.913189 at 70iterations 2.9782573E-02 0.8131750 at 80iterations 1.4495663E-02 0.4380035 at 90iterations 7.0311106E-03 0.2233582 at 100iterations 3.4303186E-03 0.1047788 at 110iterations 1.6833304E-03 4.6482086E-02 at 120iterations finished qdiffx linear iterations at : 03:40:45 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 1.6833304E-03 4.6482086E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 03:40:46 9.547u 0.308s 0:10.33 95.2% 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 Oct 11 2011 at 03:40:46 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 = 2649 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: 2.985965 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): -14.85600 33.84000 ymin,ymax (A): 7.072999 55.57000 zmin,zma (A): 25.94700 79.59800 x,y,z range (A): 48.69600 48.49700 53.65100 scale (grids/A): 2.985965 object centre (A): 9.492001 31.32150 52.77250 number of atom coordinates read : 2649 total number of charged atoms : 2501 net assigned charge : 2.500012 assigned positive charge : 400.5259 centred at (gu) : 89.79464 90.90211 83.36411 assigned negative charge : -398.0264 centred at (gu) : 90.82173 90.04729 83.61635 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 196213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22341 grid for indexing accessible points = 1.400000 m= 103725 mr = 145766 m= 39547 mr = 86600 m= 10442 mr = 32555 m= 1870 mr = 8048 m= 132 mr = 1362 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 4609 time to turn everything in is 1.950000 number of dielectric boundary points 77533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 20004 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) : 1.990643 object centre at (A) : 9.492001 31.32150 52.77250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1950174 -0.3617740 midg,1,midg; midg,igrid,midg -0.1999885 0.5362539 1,midg,midg; igrid,midg,midg 0.5531586 -0.1188101 gauss-seidel spectral radius is 0.9992838 estimated iterations to convergence 295 setup time was (sec) 2.280000 now iterating at: 03:40:48 rms-change max change #iterations 10.76458 549.7001 at 10iterations 6.327067 136.1005 at 20iterations 3.714159 67.75122 at 30iterations 2.172498 43.56088 at 40iterations 1.272054 24.38899 at 50iterations 0.7421920 14.25771 at 60iterations 0.4335375 7.630916 at 70iterations 0.2526975 4.934509 at 80iterations 0.1474616 2.670135 at 90iterations 8.5830562E-02 1.413307 at 100iterations 4.9997058E-02 0.8562584 at 110iterations 2.9116780E-02 0.4818687 at 120iterations 1.6963739E-02 0.2756844 at 130iterations 9.9242236E-03 0.1689034 at 140iterations 5.8207903E-03 0.1024551 at 150iterations 3.4391449E-03 6.2026024E-02 at 160iterations 2.0641109E-03 3.5865784E-02 at 170iterations 1.2600404E-03 2.4370193E-02 at 180iterations finished qdiffx linear iterations at : 03:41:02 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 1.2600404E-03 2.4370193E-02 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.20000 DelPhi exited at 03:41:03 16.204u 0.326s 0:17.10 96.6% 0+0k 0+0io 0pf+0w