Sun Oct 9 14:36:19 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 Sun Oct 9 2011 at 14:36:19 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 = 1365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.9086037 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): -1.641000 37.54000 ymin,ymax (A): -13.88400 21.09300 zmin,zma (A): -14.33100 23.20400 x,y,z range (A): 39.18100 34.97700 37.53500 scale (grids/A): 0.9086037 object centre (A): 17.94950 3.604500 4.436501 number of atom coordinates read : 1365 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 89.81641 90.37637 90.78561 assigned negative charge : -204.4291 centred at (gu) : 89.46126 90.32950 90.93875 start vw surface at 0.1200000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7971 nv = 96 ne = 84 npr = 28708 no. pairs analyzed = 28708 no. exposed pairs = 1667 no. arc points = 12208 no. surface atoms = 560 nbur = 805 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 844 mr = 4661 m= 9 mr = 266 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 666 ## 48 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6758 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2966908E-06 -2.0482505E-06 midg,1,midg; midg,igrid,midg -6.1256509E-07 3.7589038E-07 1,midg,midg; igrid,midg,midg -4.1787589E-06 3.4435909E-06 gauss-seidel spectral radius is 0.9935948 estimated iterations to convergence 101 setup time was (sec) 0.4600000 now iterating at: 14:36:19 rms-change max change #iterations 0.4207838 69.29684 at 10iterations 8.0600590E-02 10.19701 at 20iterations 1.5784025E-02 1.781651 at 30iterations 3.0220586E-03 0.4169579 at 40iterations 5.8590405E-04 7.6866150E-02 at 50iterations finished qdiffx linear iterations at : 14:36:22 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 5.8590405E-04 7.6866150E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 14:36:22 3.166u 0.146s 0:03.59 91.9% 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 Sun Oct 9 2011 at 14:36:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1365 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: 2.725811 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): -1.641000 37.54000 ymin,ymax (A): -13.88400 21.09300 zmin,zma (A): -14.33100 23.20400 x,y,z range (A): 39.18100 34.97700 37.53500 scale (grids/A): 2.725811 object centre (A): 17.94950 3.604500 4.436501 number of atom coordinates read : 1365 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 89.44946 91.12943 92.35709 assigned negative charge : -204.4291 centred at (gu) : 88.38390 90.98870 92.81628 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12208 grid for indexing accessible points = 1.400000 m= 37873 mr = 57096 m= 11862 mr = 30258 m= 2320 mr = 8891 m= 220 mr = 1510 m= 5 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 35766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 10021 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) : 0.9086037 object centre at (A) : 17.94950 3.604500 4.436501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7347539E-02 2.1767791E-02 midg,1,midg; midg,igrid,midg -6.5515958E-02 -8.8165551E-02 1,midg,midg; igrid,midg,midg -2.3930045E-03 0.1130619 gauss-seidel spectral radius is 0.9991462 estimated iterations to convergence 270 setup time was (sec) 0.9500000 now iterating at: 14:36:23 rms-change max change #iterations 5.523891 247.6002 at 10iterations 3.055028 96.87264 at 20iterations 1.673892 47.86014 at 30iterations 0.9200346 25.67184 at 40iterations 0.5061445 13.52487 at 50iterations 0.2781647 7.287117 at 60iterations 0.1525354 3.699253 at 70iterations 8.3806738E-02 2.153659 at 80iterations 4.5965068E-02 1.235442 at 90iterations 2.5229309E-02 0.6363229 at 100iterations 1.3803610E-02 0.3718119 at 110iterations 7.5883255E-03 0.1906567 at 120iterations finished qdiffx linear iterations at : 14:36:29 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 7.5883255E-03 0.1906567 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 14:36:30 7.097u 0.158s 0:07.53 96.1% 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 14:36:30 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 = 1365 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: 4.088717 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): -1.641000 37.54000 ymin,ymax (A): -13.88400 21.09300 zmin,zma (A): -14.33100 23.20400 x,y,z range (A): 39.18100 34.97700 37.53500 scale (grids/A): 4.088717 object centre (A): 17.94950 3.604500 4.436501 number of atom coordinates read : 1365 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 89.17422 91.69426 93.53565 assigned negative charge : -204.4291 centred at (gu) : 87.57585 91.48305 94.22451 start vw surface at 0.1700000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 186411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12208 grid for indexing accessible points = 1.400000 m= 108060 mr = 136036 m= 57076 mr = 92144 m= 24354 mr = 49393 m= 8181 mr = 20073 m= 2074 mr = 6483 m= 387 mr = 1584 m= 32 mr = 270 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 80579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 10024 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) : 2.725811 object centre at (A) : 17.94950 3.604500 4.436501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4700243 0.2493600 midg,1,midg; midg,igrid,midg -0.3845054 -0.7076633 1,midg,midg; igrid,midg,midg 0.5612230 0.4851258 gauss-seidel spectral radius is 0.9993492 estimated iterations to convergence 309 setup time was (sec) 2.410000 now iterating at: 14:36:32 rms-change max change #iterations 11.05633 225.1907 at 10iterations 6.544607 123.0005 at 20iterations 3.896451 74.37294 at 30iterations 2.318658 35.95568 at 40iterations 1.374255 21.47820 at 50iterations 0.8170733 12.47141 at 60iterations 0.4862839 7.070587 at 70iterations 0.2889818 4.879264 at 80iterations 0.1717355 2.699060 at 90iterations 0.1018297 1.414413 at 100iterations 6.0704626E-02 0.8776608 at 110iterations 3.6167316E-02 0.5427427 at 120iterations 2.1538770E-02 0.3296242 at 130iterations 1.2867237E-02 0.2085161 at 140iterations 7.7367458E-03 0.1174660 at 150iterations 4.6569123E-03 8.0604553E-02 at 160iterations 2.8342386E-03 4.9926758E-02 at 170iterations 1.7513055E-03 2.9914856E-02 at 180iterations finished qdiffx linear iterations at : 14:36:42 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 1.7513055E-03 2.9914856E-02 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 14:36:42 11.948u 0.195s 0:12.42 97.6% 0+0k 0+0io 0pf+0w