Sun Oct 9 03:25:41 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 03:25:41 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5390591 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): 215.0780 275.5760 ymin,ymax (A): 73.64400 139.6850 zmin,zma (A): -70.02600 -7.953001 x,y,z range (A): 60.49800 66.04099 62.07300 scale (grids/A): 0.5390591 object centre (A): 245.3270 106.6645 -38.98950 number of atom coordinates read : 4352 total number of charged atoms : 4163 net assigned charge : 15.60002 assigned positive charge : 642.7745 centred at (gu) : 90.51745 88.15118 90.33234 assigned negative charge : -627.1788 centred at (gu) : 90.47282 88.26091 90.31067 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8040 nv = 96 ne = 84 npr = 88767 no. pairs analyzed = 88767 no. exposed pairs = 5544 no. arc points = 38539 no. surface atoms = 1890 nbur = 2462 mkacc time = 0.1900000 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 = 1.568000 m= 328 mr = 4116 m= 0 mr = 15 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3822 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1770171E-10 9.4610275E-10 midg,1,midg; midg,igrid,midg 2.3800177E-09 -4.2043421E-11 1,midg,midg; igrid,midg,midg 3.4953393E-10 1.1768523E-09 gauss-seidel spectral radius is 0.9823684 estimated iterations to convergence 62 setup time was (sec) 0.6400000 now iterating at: 03:25:42 rms-change max change #iterations 8.4639125E-02 12.29633 at 10iterations 7.3611536E-03 1.194230 at 20iterations 1.9170804E-03 0.2345390 at 30iterations 7.5965276E-04 9.2413902E-02 at 40iterations 3.1327494E-04 3.9884567E-02 at 50iterations finished qdiffx linear iterations at : 03:25:45 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 3.1327494E-04 3.9884567E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 03:25:45 3.205u 0.147s 0:03.65 91.5% 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 03:25:45 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.617177 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): 215.0780 275.5760 ymin,ymax (A): 73.64400 139.6850 zmin,zma (A): -70.02600 -7.953001 x,y,z range (A): 60.49800 66.04099 62.07300 scale (grids/A): 1.617177 object centre (A): 245.3270 106.6645 -38.98950 number of atom coordinates read : 4352 total number of charged atoms : 4163 net assigned charge : 15.60002 assigned positive charge : 642.7745 centred at (gu) : 91.55086 84.45191 90.99574 assigned negative charge : -627.1788 centred at (gu) : 91.41817 84.78246 90.93179 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88783 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38539 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 28300 mr = 59823 m= 3129 mr = 19356 m= 107 mr = 1573 m= 0 mr = 12 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1316 time to turn everything in is 0.6100000 number of dielectric boundary points 39555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 31884 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) : 0.5390591 object centre at (A) : 245.3270 106.6645 -38.98950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1248650E-02 1.2503230E-02 midg,1,midg; midg,igrid,midg 4.7004033E-02 7.9850554E-03 1,midg,midg; igrid,midg,midg -9.0392896E-05 5.1042903E-03 gauss-seidel spectral radius is 0.9982984 estimated iterations to convergence 192 setup time was (sec) 0.8700000 now iterating at: 03:25:46 rms-change max change #iterations 4.033219 202.1513 at 10iterations 1.715864 56.53410 at 20iterations 0.7389723 25.83000 at 30iterations 0.3174569 9.696928 at 40iterations 0.1364649 4.724976 at 50iterations 5.9182461E-02 1.852108 at 60iterations 2.5747256E-02 0.8707809 at 70iterations 1.1441224E-02 0.3795166 at 80iterations 5.3892345E-03 0.1878986 at 90iterations 2.8206736E-03 8.7696075E-02 at 100iterations 1.6497250E-03 5.0025940E-02 at 110iterations 1.0880951E-03 3.1898499E-02 at 120iterations finished qdiffx linear iterations at : 03:25:52 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.0880951E-03 3.1898499E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 03:25:53 7.034u 0.172s 0:07.47 96.3% 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 03:25:53 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 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: 2.425766 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): 215.0780 275.5760 ymin,ymax (A): 73.64400 139.6850 zmin,zma (A): -70.02600 -7.953001 x,y,z range (A): 60.49800 66.04099 62.07300 scale (grids/A): 2.425766 object centre (A): 245.3270 106.6645 -38.98950 number of atom coordinates read : 4352 total number of charged atoms : 4163 net assigned charge : 15.60002 assigned positive charge : 642.7745 centred at (gu) : 92.32582 81.67754 91.49311 assigned negative charge : -627.1788 centred at (gu) : 92.12707 82.17350 91.39754 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 206465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38539 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 95882 mr = 146706 m= 28558 mr = 75305 m= 5038 mr = 21406 m= 414 mr = 3376 m= 12 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 4368 time to turn everything in is 1.460000 number of dielectric boundary points 89370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 33269 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) : 1.617177 object centre at (A) : 245.3270 106.6645 -38.98950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2143695 0.1339477 midg,1,midg; midg,igrid,midg 0.6614433 0.1262654 1,midg,midg; igrid,midg,midg 3.5642125E-02 -1.7948404E-02 gauss-seidel spectral radius is 0.9992095 estimated iterations to convergence 281 setup time was (sec) 1.740000 now iterating at: 03:25:55 rms-change max change #iterations 10.59383 324.8013 at 10iterations 6.188623 153.4916 at 20iterations 3.589613 92.92099 at 30iterations 2.067487 44.83474 at 40iterations 1.185596 26.98426 at 50iterations 0.6787637 14.10397 at 60iterations 0.3868707 7.535271 at 70iterations 0.2202088 4.322981 at 80iterations 0.1252753 2.336685 at 90iterations 7.1045473E-02 1.468515 at 100iterations 4.0297031E-02 0.7691135 at 110iterations 2.2868725E-02 0.4331923 at 120iterations 1.3050887E-02 0.2263098 at 130iterations 7.4675526E-03 0.1485329 at 140iterations 4.3253945E-03 7.4781418E-02 at 150iterations 2.5496143E-03 4.9751282E-02 at 160iterations 1.5622919E-03 2.8648376E-02 at 170iterations 1.0108935E-03 1.9896030E-02 at 180iterations finished qdiffx linear iterations at : 03:26:04 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.0108935E-03 1.9896030E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 03:26:05 11.618u 0.177s 0:12.10 97.3% 0+0k 0+0io 0pf+0w