Mon Oct 10 17:13:37 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 Mon Oct 10 2011 at 17:13:37 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 = 2874 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: 0.5668699 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): -30.70800 32.09300 ymin,ymax (A): -24.96600 24.76500 zmin,zma (A): -8.972000 37.86600 x,y,z range (A): 62.80100 49.73100 46.83800 scale (grids/A): 0.5668699 object centre (A): 0.6925011 -0.1005001 14.44700 number of atom coordinates read : 2874 total number of charged atoms : 2733 net assigned charge : -0.9999746 assigned positive charge : 431.1011 centred at (gu) : 90.74467 90.05815 89.59404 assigned negative charge : -432.1023 centred at (gu) : 90.69098 89.89468 89.46079 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5927 nv = 96 ne = 84 npr = 57878 no. pairs analyzed = 57878 no. exposed pairs = 3794 no. arc points = 26431 no. surface atoms = 1277 nbur = 1597 mkacc time = 9.0000004E-02 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 = 1.540000 m= 266 mr = 2984 m= 0 mr = 6 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2200000 number of dielectric boundary points 3203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2718 ## 341 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1959761E-09 1.5078390E-09 midg,1,midg; midg,igrid,midg -2.3849709E-09 2.0937039E-09 1,midg,midg; igrid,midg,midg -7.3035633E-10 7.1953854E-10 gauss-seidel spectral radius is 0.9839375 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 17:13:38 rms-change max change #iterations 8.5719675E-02 14.42546 at 10iterations 6.2478352E-03 1.252602 at 20iterations 4.6120855E-04 7.6759338E-02 at 30iterations 3.3987835E-05 4.7721863E-03 at 40iterations 2.5474878E-06 4.4250488E-04 at 50iterations finished qdiffx linear iterations at : 17:13:41 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.5474878E-06 4.4250488E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:13:41 3.444u 0.185s 0:03.95 91.6% 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 Mon Oct 10 2011 at 17:13:41 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 = 2874 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: 1.700610 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): -30.70800 32.09300 ymin,ymax (A): -24.96600 24.76500 zmin,zma (A): -8.972000 37.86600 x,y,z range (A): 62.80100 49.73100 46.83800 scale (grids/A): 1.700610 object centre (A): 0.6925011 -0.1005001 14.44700 number of atom coordinates read : 2874 total number of charged atoms : 2733 net assigned charge : -0.9999746 assigned positive charge : 431.1011 centred at (gu) : 92.23350 90.17365 88.78158 assigned negative charge : -432.1023 centred at (gu) : 92.07277 89.68359 88.38206 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 64743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26431 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20276 mr = 42637 m= 2325 mr = 13716 m= 65 mr = 1239 m= 0 mr = 10 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1273 time to turn everything in is 0.3500000 number of dielectric boundary points 29807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21071 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) : 0.5668699 object centre at (A) : 0.6925011 -0.1005001 14.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8038699E-03 7.2022839E-03 midg,1,midg; midg,igrid,midg -2.4279704E-02 1.0023305E-02 1,midg,midg; igrid,midg,midg -9.4910320E-03 2.2329582E-02 gauss-seidel spectral radius is 0.9983192 estimated iterations to convergence 194 setup time was (sec) 0.5700000 now iterating at: 17:13:42 rms-change max change #iterations 3.550357 179.6224 at 10iterations 1.521922 56.91644 at 20iterations 0.6523786 25.31102 at 30iterations 0.2807253 10.65349 at 40iterations 0.1210767 4.105151 at 50iterations 5.2095246E-02 1.908157 at 60iterations 2.2452766E-02 0.9513531 at 70iterations 9.6207988E-03 0.4177876 at 80iterations 4.1514691E-03 0.1504211 at 90iterations 1.7912922E-03 6.4633548E-02 at 100iterations 7.7203818E-04 2.7439117E-02 at 110iterations 3.3344232E-04 1.1770248E-02 at 120iterations finished qdiffx linear iterations at : 17:13:49 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 3.3344232E-04 1.1770248E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 17:13:50 7.817u 0.190s 0:08.38 95.4% 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 Mon Oct 10 2011 at 17:13:50 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 = 2874 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: 2.550915 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): -30.70800 32.09300 ymin,ymax (A): -24.96600 24.76500 zmin,zma (A): -8.972000 37.86600 x,y,z range (A): 62.80100 49.73100 46.83800 scale (grids/A): 2.550915 object centre (A): 0.6925011 -0.1005001 14.44700 number of atom coordinates read : 2874 total number of charged atoms : 2733 net assigned charge : -0.9999746 assigned positive charge : 431.1011 centred at (gu) : 93.34998 90.26036 88.17215 assigned negative charge : -432.1023 centred at (gu) : 93.10906 89.52525 87.57293 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26431 grid for indexing accessible points = 1.400000 m= 68638 mr = 104340 m= 20598 mr = 53638 m= 3739 mr = 15337 m= 318 mr = 2528 m= 2 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4086 time to turn everything in is 0.7900000 number of dielectric boundary points 67463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21841 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) : 1.700610 object centre at (A) : 0.6925011 -0.1005001 14.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1037142E-02 7.3732778E-02 midg,1,midg; midg,igrid,midg -0.3040017 0.1641306 1,midg,midg; igrid,midg,midg 6.9706030E-02 0.4193025 gauss-seidel spectral radius is 0.9991798 estimated iterations to convergence 276 setup time was (sec) 1.010000 now iterating at: 17:13:51 rms-change max change #iterations 9.101377 339.0263 at 10iterations 5.181319 124.4733 at 20iterations 2.936822 74.32268 at 30iterations 1.658998 39.12995 at 40iterations 0.9348308 21.35947 at 50iterations 0.5238952 14.75922 at 60iterations 0.2939677 6.433645 at 70iterations 0.1648000 3.443106 at 80iterations 9.2196211E-02 1.976979 at 90iterations 5.1447820E-02 1.112421 at 100iterations 2.8782343E-02 0.5941553 at 110iterations 1.6071662E-02 0.3461599 at 120iterations 8.9752330E-03 0.1820574 at 130iterations 5.0037713E-03 0.1155472 at 140iterations 2.7813842E-03 5.7424545E-02 at 150iterations 1.5535215E-03 3.4001350E-02 at 160iterations 8.6757250E-04 1.7175674E-02 at 170iterations 4.8361754E-04 1.0255814E-02 at 180iterations finished qdiffx linear iterations at : 17:14:02 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 4.8361754E-04 1.0255814E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 17:14:03 12.305u 0.229s 0:13.10 95.5% 0+0k 0+0io 0pf+0w