Sun Oct 9 16:59:18 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 16:59:18 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4747 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: 0.5135084 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 0.5135084 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500050 assigned positive charge : 719.3699 centred at (gu) : 89.85413 90.59525 91.17236 assigned negative charge : -711.8746 centred at (gu) : 89.92995 90.67149 91.06736 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7840 nv = 96 ne = 84 npr = 96737 no. pairs analyzed = 96737 no. exposed pairs = 5651 no. arc points = 38846 no. surface atoms = 1906 nbur = 2841 mkacc time = 0.1700000 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 = 1.680000 m= 263 mr = 4251 m= 0 mr = 7 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3200000 number of dielectric boundary points 3845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3897 ## 590 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4021492E-10 5.7407412E-10 midg,1,midg; midg,igrid,midg 2.9007360E-10 -1.2620233E-10 1,midg,midg; igrid,midg,midg 3.5084205E-10 -1.0132216E-10 gauss-seidel spectral radius is 0.9805956 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 16:59:19 rms-change max change #iterations 7.1404792E-02 11.54188 at 10iterations 5.6088292E-03 0.8259497 at 20iterations 1.3779635E-03 0.2185879 at 30iterations 5.4031744E-04 9.1856003E-02 at 40iterations 2.2099691E-04 3.8745880E-02 at 50iterations finished qdiffx linear iterations at : 16:59:22 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.2099691E-04 3.8745880E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 16:59:22 3.558u 0.159s 0:03.99 92.7% 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 16:59:22 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.540525 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 1.540525 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500050 assigned positive charge : 719.3699 centred at (gu) : 89.56103 91.78444 93.51575 assigned negative charge : -711.8746 centred at (gu) : 89.78938 92.01381 93.20195 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 89399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38846 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25341 mr = 62843 m= 2002 mr = 17017 m= 38 mr = 900 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 372 time to turn everything in is 0.4300000 number of dielectric boundary points 36020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 556 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 34563 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) : 0.5135084 object centre at (A) : 35.26750 26.65300 -1.297501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3831096E-02 3.5736259E-02 midg,1,midg; midg,igrid,midg 9.0631079E-03 -2.0095457E-03 1,midg,midg; igrid,midg,midg 2.2686172E-02 -2.1033806E-03 gauss-seidel spectral radius is 0.9981237 estimated iterations to convergence 183 setup time was (sec) 0.6500000 now iterating at: 16:59:23 rms-change max change #iterations 3.798653 144.2473 at 10iterations 1.556253 60.61401 at 20iterations 0.6442772 19.37970 at 30iterations 0.2640191 8.521400 at 40iterations 0.1094219 4.197044 at 50iterations 4.5144424E-02 1.394852 at 60iterations 1.8879974E-02 0.5646791 at 70iterations 8.1182709E-03 0.2661848 at 80iterations 3.7526307E-03 0.1429234 at 90iterations 1.9571325E-03 6.9847107E-02 at 100iterations 1.1803191E-03 4.4467926E-02 at 110iterations 7.8895874E-04 2.7648926E-02 at 120iterations finished qdiffx linear iterations at : 16:59:30 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 7.8895874E-04 2.7648926E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 16:59:30 7.928u 0.202s 0:08.38 96.8% 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 16:59:30 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4747 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: 2.310788 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 2.310788 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500050 assigned positive charge : 719.3699 centred at (gu) : 89.34119 92.67627 95.27303 assigned negative charge : -711.8746 centred at (gu) : 89.68389 93.02082 94.80300 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 208884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38846 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91851 mr = 154260 m= 22356 mr = 72463 m= 2909 mr = 16363 m= 147 mr = 1825 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 1275 time to turn everything in is 1.040000 number of dielectric boundary points 81183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 36645 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) : 1.540525 object centre at (A) : 35.26750 26.65300 -1.297501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2393944 0.6189957 midg,1,midg; midg,igrid,midg 0.1277886 -4.1512325E-02 1,midg,midg; igrid,midg,midg 0.4092785 2.1922009E-04 gauss-seidel spectral radius is 0.9991598 estimated iterations to convergence 272 setup time was (sec) 1.280000 now iterating at: 16:59:32 rms-change max change #iterations 10.24373 272.5395 at 10iterations 5.879028 128.4256 at 20iterations 3.346674 72.72324 at 30iterations 1.889711 38.88469 at 40iterations 1.064492 21.69277 at 50iterations 0.5976112 13.06092 at 60iterations 0.3348973 6.959485 at 70iterations 0.1869093 3.693884 at 80iterations 0.1044039 1.952454 at 90iterations 5.8258962E-02 1.101318 at 100iterations 3.2427810E-02 0.6436920 at 110iterations 1.8090768E-02 0.3725281 at 120iterations 1.0102079E-02 0.2082672 at 130iterations 5.6682723E-03 0.1107500 at 140iterations 3.1948518E-03 5.6709290E-02 at 150iterations 1.8250522E-03 3.6453247E-02 at 160iterations 1.0652877E-03 2.4883270E-02 at 170iterations 6.4580759E-04 1.2535095E-02 at 180iterations finished qdiffx linear iterations at : 16:59:43 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 6.4580759E-04 1.2535095E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 16:59:44 12.937u 0.186s 0:13.38 97.9% 0+0k 0+0io 0pf+0w