Sun Oct 9 08:48:57 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 08:48:57 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5859 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5005625 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): 3.773000 74.89300 ymin,ymax (A): 17.68400 85.56100 zmin,zma (A): 6.552000 75.18800 x,y,z range (A): 71.12000 67.87700 68.63600 scale (grids/A): 0.5005625 object centre (A): 39.33300 51.62250 40.87000 number of atom coordinates read : 5859 total number of charged atoms : 5689 net assigned charge : -4.985974 assigned positive charge : 882.0774 centred at (gu) : 89.88647 89.15170 89.21776 assigned negative charge : -887.0707 centred at (gu) : 89.81246 89.12322 89.15968 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9149 nv = 96 ne = 84 npr = 118383 no. pairs analyzed = 118383 no. exposed pairs = 7341 no. arc points = 50509 no. surface atoms = 2452 nbur = 3407 mkacc time = 0.2100000 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= 299 mr = 4691 m= 1 mr = 4 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 0.3800000 number of dielectric boundary points 4754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4890 ## 738 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 12397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0336718E-10 6.1803049E-11 midg,1,midg; midg,igrid,midg -1.2852611E-10 1.2389690E-11 1,midg,midg; igrid,midg,midg -2.0442108E-10 1.0594161E-10 gauss-seidel spectral radius is 0.9796687 estimated iterations to convergence 58 setup time was (sec) 0.5900000 now iterating at: 08:48:58 rms-change max change #iterations 6.8607815E-02 8.667465 at 10iterations 3.7660371E-03 0.5483055 at 20iterations 3.2138356E-04 6.6267014E-02 at 30iterations 7.6282311E-05 1.7568588E-02 at 40iterations 2.3336172E-05 5.1097870E-03 at 50iterations finished qdiffx linear iterations at : 08:49:01 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 2.3336172E-05 5.1097870E-03 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 08:49:01 3.843u 0.226s 0:04.33 93.7% 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 08:49:01 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5859 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.501687 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): 3.773000 74.89300 ymin,ymax (A): 17.68400 85.56100 zmin,zma (A): 6.552000 75.18800 x,y,z range (A): 71.12000 67.87700 68.63600 scale (grids/A): 1.501687 object centre (A): 39.33300 51.62250 40.87000 number of atom coordinates read : 5859 total number of charged atoms : 5689 net assigned charge : -4.985974 assigned positive charge : 882.0774 centred at (gu) : 89.65746 87.45348 87.65155 assigned negative charge : -887.0707 centred at (gu) : 89.43748 87.36932 87.47841 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50509 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 29005 mr = 71570 m= 2265 mr = 18788 m= 25 mr = 919 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1279 time to turn everything in is 0.5200000 number of dielectric boundary points 44415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 752 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 42383 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) : 0.5005625 object centre at (A) : 39.33300 51.62250 40.87000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4263385E-02 -1.0154041E-02 midg,1,midg; midg,igrid,midg -6.1338223E-03 -1.9388236E-03 1,midg,midg; igrid,midg,midg -9.8028770E-03 2.1911096E-02 gauss-seidel spectral radius is 0.9981268 estimated iterations to convergence 184 setup time was (sec) 0.7700000 now iterating at: 08:49:02 rms-change max change #iterations 4.105452 196.9950 at 10iterations 1.695553 51.08502 at 20iterations 0.6965481 22.20279 at 30iterations 0.2871762 8.485893 at 40iterations 0.1185537 3.652546 at 50iterations 4.8847966E-02 1.472481 at 60iterations 2.0175816E-02 0.6020241 at 70iterations 8.3502624E-03 0.2575648 at 80iterations 3.4489990E-03 0.1049747 at 90iterations 1.4339547E-03 4.6180725E-02 at 100iterations 5.9891795E-04 1.8141270E-02 at 110iterations 2.5573545E-04 8.6822510E-03 at 120iterations finished qdiffx linear iterations at : 08:49:10 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 2.5573545E-04 8.6822510E-03 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.650000 DelPhi exited at 08:49:11 8.648u 0.235s 0:09.36 94.7% 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 08:49:11 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5859 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.252531 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): 3.773000 74.89300 ymin,ymax (A): 17.68400 85.56100 zmin,zma (A): 6.552000 75.18800 x,y,z range (A): 71.12000 67.87700 68.63600 scale (grids/A): 2.252531 object centre (A): 39.33300 51.62250 40.87000 number of atom coordinates read : 5859 total number of charged atoms : 5689 net assigned charge : -4.985974 assigned positive charge : 882.0774 centred at (gu) : 89.48587 86.17997 86.47694 assigned negative charge : -887.0707 centred at (gu) : 89.15619 86.05381 86.21747 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 243768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50509 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 106457 mr = 176557 m= 24670 mr = 81902 m= 2990 mr = 17370 m= 125 mr = 1843 m= 0 mr = 38 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 4333 time to turn everything in is 1.250000 number of dielectric boundary points 100300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 45344 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) : 1.501687 object centre at (A) : 39.33300 51.62250 40.87000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3894676 -0.1865190 midg,1,midg; midg,igrid,midg -0.1625263 -2.0144973E-02 1,midg,midg; igrid,midg,midg -2.2930769E-02 0.5579093 gauss-seidel spectral radius is 0.9991973 estimated iterations to convergence 279 setup time was (sec) 1.520000 now iterating at: 08:49:12 rms-change max change #iterations 11.34076 271.9149 at 10iterations 6.596080 154.6854 at 20iterations 3.816321 85.62585 at 30iterations 2.194164 46.47645 at 40iterations 1.257619 25.39346 at 50iterations 0.7206081 13.77956 at 60iterations 0.4108864 7.375687 at 70iterations 0.2332910 4.457334 at 80iterations 0.1329063 2.434107 at 90iterations 7.5348184E-02 1.352251 at 100iterations 4.2623583E-02 0.7603779 at 110iterations 2.4179686E-02 0.4227755 at 120iterations 1.3664100E-02 0.2545824 at 130iterations 7.7343248E-03 0.1340733 at 140iterations 4.3656561E-03 8.6930275E-02 at 150iterations 2.4656723E-03 4.2768478E-02 at 160iterations 1.3901272E-03 2.3004532E-02 at 170iterations 7.8584638E-04 1.4397383E-02 at 180iterations finished qdiffx linear iterations at : 08:49:25 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 7.8584638E-04 1.4397383E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.09000 DelPhi exited at 08:49:25 14.093u 0.232s 0:14.65 97.7% 0+0k 0+0io 0pf+0w