Tue Oct 11 05:26:51 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 Tue Oct 11 2011 at 05:26:51 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 = 2007 !!! WARNING: MG8 872 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7174816 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): 25.75000 72.52300 ymin,ymax (A): -20.50600 29.11200 zmin,zma (A): 3.922000 46.51600 x,y,z range (A): 46.77300 49.61800 42.59400 scale (grids/A): 0.7174816 object centre (A): 49.13650 4.302999 25.21900 number of atom coordinates read : 2007 total number of charged atoms : 1930 net assigned charge : 8.900008 assigned positive charge : 312.6470 centred at (gu) : 89.07264 91.17901 90.15184 assigned negative charge : -303.7472 centred at (gu) : 89.20601 91.07303 90.20941 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7190 nv = 96 ne = 84 npr = 39065 no. pairs analyzed = 39065 no. exposed pairs = 2489 no. arc points = 17190 no. surface atoms = 851 nbur = 1156 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4113 m= 5 mr = 101 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 0.2700000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1631 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2392839E-07 6.0090876E-08 midg,1,midg; midg,igrid,midg 2.4072127E-08 1.9559978E-07 1,midg,midg; igrid,midg,midg 2.0561943E-07 1.1031942E-08 gauss-seidel spectral radius is 0.9898667 estimated iterations to convergence 81 setup time was (sec) 0.5100000 now iterating at: 05:26:52 rms-change max change #iterations 0.2092037 29.02119 at 10iterations 2.6453350E-02 3.688840 at 20iterations 3.5004029E-03 0.4538002 at 30iterations 5.1213318E-04 6.6263199E-02 at 40iterations 1.0305014E-04 1.2535095E-02 at 50iterations finished qdiffx linear iterations at : 05:26:55 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.0305014E-04 1.2535095E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 05:26:55 3.476u 0.179s 0:03.96 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 Tue Oct 11 2011 at 05:26:55 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 = 2007 !!! WARNING: MG8 872 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.152445 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): 25.75000 72.52300 ymin,ymax (A): -20.50600 29.11200 zmin,zma (A): 3.922000 46.51600 x,y,z range (A): 46.77300 49.61800 42.59400 scale (grids/A): 2.152445 object centre (A): 49.13650 4.302999 25.21900 number of atom coordinates read : 2007 total number of charged atoms : 1930 net assigned charge : 8.900008 assigned positive charge : 312.6470 centred at (gu) : 87.21796 93.53714 90.45567 assigned negative charge : -303.7472 centred at (gu) : 87.61816 93.21922 90.62824 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17190 grid for indexing accessible points = 1.400000 m= 31559 mr = 53427 m= 6499 mr = 24189 m= 586 mr = 4385 m= 19 mr = 275 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15338 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) : 0.7174816 object centre at (A) : 49.13650 4.302999 25.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1629942E-02 3.5758991E-02 midg,1,midg; midg,igrid,midg 3.8221888E-02 0.1128632 1,midg,midg; igrid,midg,midg 5.3142015E-02 -3.4502152E-02 gauss-seidel spectral radius is 0.9988564 estimated iterations to convergence 234 setup time was (sec) 0.8800000 now iterating at: 05:26:56 rms-change max change #iterations 4.673881 191.8209 at 10iterations 2.329491 74.38524 at 20iterations 1.164843 37.69535 at 30iterations 0.5839220 19.06222 at 40iterations 0.2924733 8.874378 at 50iterations 0.1456856 4.494365 at 60iterations 7.2822228E-02 2.499463 at 70iterations 3.6575899E-02 1.110355 at 80iterations 1.8368511E-02 0.5559750 at 90iterations 9.1964165E-03 0.3092499 at 100iterations 4.6423031E-03 0.1390648 at 110iterations 2.3710667E-03 6.5979004E-02 at 120iterations finished qdiffx linear iterations at : 05:27:03 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 2.3710667E-03 6.5979004E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 05:27:03 7.541u 0.178s 0:08.33 92.5% 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 Tue Oct 11 2011 at 05:27:04 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 = 2007 !!! WARNING: MG8 872 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.228667 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): 25.75000 72.52300 ymin,ymax (A): -20.50600 29.11200 zmin,zma (A): 3.922000 46.51600 x,y,z range (A): 46.77300 49.61800 42.59400 scale (grids/A): 3.228667 object centre (A): 49.13650 4.302999 25.21900 number of atom coordinates read : 2007 total number of charged atoms : 1930 net assigned charge : 8.900008 assigned positive charge : 312.6470 centred at (gu) : 85.82695 95.30571 90.68357 assigned negative charge : -303.7472 centred at (gu) : 86.42721 94.82886 90.94241 start vw surface at 0.1500000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 173876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17190 grid for indexing accessible points = 1.400000 m= 96853 mr = 128551 m= 41204 mr = 80755 m= 12205 mr = 34092 m= 2451 mr = 9601 m= 261 mr = 1746 m= 16 mr = 166 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 71948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 15440 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) : 2.152445 object centre at (A) : 49.13650 4.302999 25.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1866882 0.2936012 midg,1,midg; midg,igrid,midg 0.2683108 1.048411 1,midg,midg; igrid,midg,midg 0.4696359 -0.3951143 gauss-seidel spectral radius is 0.9993078 estimated iterations to convergence 300 setup time was (sec) 2.200000 now iterating at: 05:27:06 rms-change max change #iterations 10.44763 356.0804 at 10iterations 6.219290 143.4948 at 20iterations 3.700959 72.24472 at 30iterations 2.199071 44.98871 at 40iterations 1.304094 24.59652 at 50iterations 0.7709735 14.89174 at 60iterations 0.4547818 8.306487 at 70iterations 0.2687579 5.662073 at 80iterations 0.1582914 2.836777 at 90iterations 9.3553133E-02 1.755127 at 100iterations 5.5055574E-02 1.066326 at 110iterations 3.2555003E-02 0.5712271 at 120iterations 1.9373912E-02 0.3472061 at 130iterations 1.1660850E-02 0.2233067 at 140iterations 7.1298871E-03 0.1374760 at 150iterations 4.5131017E-03 8.0811501E-02 at 160iterations 3.0060508E-03 5.2936554E-02 at 170iterations 2.1210888E-03 3.6514282E-02 at 180iterations finished qdiffx linear iterations at : 05:27:17 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 2.1210888E-03 3.6514282E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 05:27:18 13.580u 0.161s 0:14.07 97.6% 0+0k 0+0io 0pf+0w