Sun Oct 9 18:17:32 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 18:17:32 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 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: 0.5578713 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): -8.103000 55.71100 ymin,ymax (A): -14.45000 34.11000 zmin,zma (A): 22.43800 70.51200 x,y,z range (A): 63.81400 48.56000 48.07400 scale (grids/A): 0.5578713 object centre (A): 23.80400 9.830000 46.47500 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000027 assigned positive charge : 442.3544 centred at (gu) : 90.25761 90.64784 88.64053 assigned negative charge : -436.3553 centred at (gu) : 90.31909 90.73248 88.56508 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5966 nv = 96 ne = 84 npr = 56934 no. pairs analyzed = 56934 no. exposed pairs = 3791 no. arc points = 26390 no. surface atoms = 1284 nbur = 1612 mkacc time = 0.1400000 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= 278 mr = 3053 m= 0 mr = 10 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2655 ## 318 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7634 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3399202E-10 9.8149122E-10 midg,1,midg; midg,igrid,midg 1.2406490E-09 -3.0060718E-10 1,midg,midg; igrid,midg,midg 1.1482669E-09 -1.7213205E-11 gauss-seidel spectral radius is 0.9834220 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 18:17:33 rms-change max change #iterations 7.9130538E-02 13.66541 at 10iterations 5.8361315E-03 1.060539 at 20iterations 7.0806802E-04 0.1230507 at 30iterations 2.4701716E-04 3.6064148E-02 at 40iterations 1.2166820E-04 1.7409801E-02 at 50iterations finished qdiffx linear iterations at : 18:17:36 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.2166820E-04 1.7409801E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 18:17:36 3.374u 0.148s 0:03.87 90.6% 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 Sun Oct 9 2011 at 18:17:36 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 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: 1.673614 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): -8.103000 55.71100 ymin,ymax (A): -14.45000 34.11000 zmin,zma (A): 22.43800 70.51200 x,y,z range (A): 63.81400 48.56000 48.07400 scale (grids/A): 1.673614 object centre (A): 23.80400 9.830000 46.47500 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000027 assigned positive charge : 442.3544 centred at (gu) : 90.77229 91.94279 85.92078 assigned negative charge : -436.3553 centred at (gu) : 90.95704 92.19730 85.69501 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21848 mr = 44844 m= 2731 mr = 14831 m= 108 mr = 1366 m= 0 mr = 20 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 243 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21218 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) : 0.5578713 object centre at (A) : 23.80400 9.830000 46.47500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5303946E-03 6.6423751E-03 midg,1,midg; midg,igrid,midg 8.6074229E-03 -8.1432285E-03 1,midg,midg; igrid,midg,midg 2.4115218E-02 -6.9859871E-03 gauss-seidel spectral radius is 0.9982674 estimated iterations to convergence 191 setup time was (sec) 0.7800000 now iterating at: 18:17:37 rms-change max change #iterations 3.525807 157.2736 at 10iterations 1.497321 61.95248 at 20iterations 0.6397552 23.85409 at 30iterations 0.2728183 9.502289 at 40iterations 0.1165768 4.074890 at 50iterations 4.9974903E-02 1.758480 at 60iterations 2.1392055E-02 0.7525187 at 70iterations 9.1558816E-03 0.3136330 at 80iterations 3.9860005E-03 0.1608019 at 90iterations 1.8047709E-03 6.7924500E-02 at 100iterations 8.9167425E-04 3.6051750E-02 at 110iterations 5.2098016E-04 1.7953873E-02 at 120iterations finished qdiffx linear iterations at : 18:17:44 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 5.2098016E-04 1.7953873E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 18:17:44 7.556u 0.171s 0:08.04 96.0% 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 18:17:44 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 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: 2.510421 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): -8.103000 55.71100 ymin,ymax (A): -14.45000 34.11000 zmin,zma (A): 22.43800 70.51200 x,y,z range (A): 63.81400 48.56000 48.07400 scale (grids/A): 2.510421 object centre (A): 23.80400 9.830000 46.47500 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000027 assigned positive charge : 442.3544 centred at (gu) : 91.15812 92.91382 83.88093 assigned negative charge : -436.3553 centred at (gu) : 91.43543 93.29566 83.54236 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 152865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26390 grid for indexing accessible points = 1.400000 m= 73502 mr = 109555 m= 22999 mr = 57690 m= 4403 mr = 17178 m= 382 mr = 2844 m= 13 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 66699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 22000 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) : 1.673614 object centre at (A) : 23.80400 9.830000 46.47500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2435424E-02 7.7444382E-02 midg,1,midg; midg,igrid,midg 0.1450147 -0.1587417 1,midg,midg; igrid,midg,midg 0.9018285 -6.3495487E-02 gauss-seidel spectral radius is 0.9991629 estimated iterations to convergence 273 setup time was (sec) 1.490000 now iterating at: 18:17:46 rms-change max change #iterations 9.098789 333.2794 at 10iterations 5.218806 143.9295 at 20iterations 2.974517 71.93008 at 30iterations 1.676313 38.68334 at 40iterations 0.9466401 20.95218 at 50iterations 0.5307015 12.41799 at 60iterations 0.2980931 7.176634 at 70iterations 0.1668008 3.539619 at 80iterations 9.3183249E-02 1.882342 at 90iterations 5.2052539E-02 1.227059 at 100iterations 2.9126646E-02 0.6089735 at 110iterations 1.6203394E-02 0.4231140 at 120iterations 9.0389159E-03 0.2137146 at 130iterations 5.0408207E-03 0.1029596 at 140iterations 2.8127967E-03 5.9202194E-02 at 150iterations 1.5704874E-03 3.4076691E-02 at 160iterations 8.7928685E-04 1.9705772E-02 at 170iterations 4.9827277E-04 9.7951889E-03 at 180iterations finished qdiffx linear iterations at : 18:17:56 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 4.9827277E-04 9.7951889E-03 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 18:17:57 11.927u 0.174s 0:12.37 97.7% 0+0k 0+0io 0pf+0w