Mon Oct 10 14:17:32 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+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 14:17:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 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: 0.5947111 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): -45.61300 5.513000 ymin,ymax (A): -43.36100 16.50000 zmin,zma (A): 40.03800 90.56800 x,y,z range (A): 51.12600 59.86100 50.53000 scale (grids/A): 0.5947111 object centre (A): -20.05000 -13.43050 65.30300 number of atom coordinates read : 2725 total number of charged atoms : 2581 net assigned charge : -5.999987 assigned positive charge : 415.8975 centred at (gu) : 91.00835 87.29042 89.09906 assigned negative charge : -421.8983 centred at (gu) : 90.91151 87.24790 89.14207 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6525 nv = 96 ne = 84 npr = 53372 no. pairs analyzed = 53372 no. exposed pairs = 3791 no. arc points = 26051 no. surface atoms = 1287 nbur = 1438 mkacc time = 0.1100000 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 = 1.456000 m= 341 mr = 3307 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2718 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6147534E-10 -2.9241105E-09 midg,1,midg; midg,igrid,midg -6.6437140E-09 -4.3166071E-10 1,midg,midg; igrid,midg,midg -4.2950412E-09 1.3504295E-09 gauss-seidel spectral radius is 0.9853867 estimated iterations to convergence 68 setup time was (sec) 0.5100000 now iterating at: 14:17:33 rms-change max change #iterations 0.1079212 16.22380 at 10iterations 8.6740013E-03 1.291669 at 20iterations 7.9368765E-04 0.1230164 at 30iterations 1.0754599E-04 1.8978119E-02 at 40iterations 2.5422742E-05 4.9438477E-03 at 50iterations finished qdiffx linear iterations at : 14:17:35 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 2.5422742E-05 4.9438477E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 14:17:36 3.119u 0.144s 0:03.62 89.7% 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 Mon Oct 10 2011 at 14:17:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.784133 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): -45.61300 5.513000 ymin,ymax (A): -43.36100 16.50000 zmin,zma (A): 40.03800 90.56800 x,y,z range (A): 51.12600 59.86100 50.53000 scale (grids/A): 1.784133 object centre (A): -20.05000 -13.43050 65.30300 number of atom coordinates read : 2725 total number of charged atoms : 2581 net assigned charge : -5.999987 assigned positive charge : 415.8975 centred at (gu) : 93.02451 81.87070 87.29645 assigned negative charge : -421.8983 centred at (gu) : 92.73415 81.74345 87.42605 start vw surface at 0.2100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26051 grid for indexing accessible points = 1.400000 m= 24478 mr = 47002 m= 3777 mr = 16997 m= 192 mr = 2211 m= 0 mr = 57 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 32635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20139 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) : 0.5947111 object centre at (A) : -20.05000 -13.43050 65.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8999130E-02 -1.2783072E-02 midg,1,midg; midg,igrid,midg -1.1844448E-03 3.4044228E-02 1,midg,midg; igrid,midg,midg -2.4554841E-02 -1.1542183E-02 gauss-seidel spectral radius is 0.9984697 estimated iterations to convergence 203 setup time was (sec) 0.8600000 now iterating at: 14:17:37 rms-change max change #iterations 3.934314 176.4219 at 10iterations 1.745587 65.91042 at 20iterations 0.7819756 31.37350 at 30iterations 0.3511665 14.38395 at 40iterations 0.1569857 5.179527 at 50iterations 7.0248418E-02 2.412312 at 60iterations 3.1458717E-02 1.043765 at 70iterations 1.4105999E-02 0.4327841 at 80iterations 6.3076885E-03 0.2179985 at 90iterations 2.8223600E-03 9.8306656E-02 at 100iterations 1.2645391E-03 4.0807724E-02 at 110iterations 5.6934782E-04 2.1865845E-02 at 120iterations finished qdiffx linear iterations at : 14:17:43 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 5.6934782E-04 2.1865845E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 14:17:43 7.086u 0.190s 0:07.60 95.6% 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 14:17:43 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 = 2725 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: 2.676200 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): -45.61300 5.513000 ymin,ymax (A): -43.36100 16.50000 zmin,zma (A): 40.03800 90.56800 x,y,z range (A): 51.12600 59.86100 50.53000 scale (grids/A): 2.676200 object centre (A): -20.05000 -13.43050 65.30300 number of atom coordinates read : 2725 total number of charged atoms : 2581 net assigned charge : -5.999987 assigned positive charge : 415.8975 centred at (gu) : 94.53661 77.80577 85.94446 assigned negative charge : -421.8983 centred at (gu) : 94.10110 77.61512 86.13898 start vw surface at 0.2000000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 162818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26051 grid for indexing accessible points = 1.400000 m= 79846 mr = 114754 m= 27692 mr = 62873 m= 6608 mr = 21299 m= 910 mr = 4804 m= 47 mr = 579 m= 0 mr = 19 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 73593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 20637 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) : 1.784133 object centre at (A) : -20.05000 -13.43050 65.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2710079 -0.1186524 midg,1,midg; midg,igrid,midg -0.2465552 0.5949180 1,midg,midg; igrid,midg,midg -0.3108052 -0.1065201 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 1.560000 now iterating at: 14:17:45 rms-change max change #iterations 9.666231 312.2694 at 10iterations 5.698141 144.9820 at 20iterations 3.297976 80.91928 at 30iterations 1.908496 38.07690 at 40iterations 1.094389 21.42915 at 50iterations 0.6259298 12.29538 at 60iterations 0.3571953 7.068214 at 70iterations 0.2037849 3.861650 at 80iterations 0.1159455 2.405302 at 90iterations 6.6051692E-02 1.313942 at 100iterations 3.7520058E-02 0.7697353 at 110iterations 2.1214319E-02 0.4046054 at 120iterations 1.2086628E-02 0.2487516 at 130iterations 6.8622436E-03 0.1311817 at 140iterations 3.8903269E-03 7.5450897E-02 at 150iterations 2.2084671E-03 4.3457031E-02 at 160iterations 1.2547842E-03 2.6046276E-02 at 170iterations 7.1333017E-04 1.3437271E-02 at 180iterations finished qdiffx linear iterations at : 14:17:55 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 7.1333017E-04 1.3437271E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 14:17:55 11.372u 0.214s 0:12.11 95.6% 0+0k 0+0io 0pf+0w