Sun Oct 9 08:58:38 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 08:58:38 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5970 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4856422 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): 14.43100 79.91700 ymin,ymax (A): 18.39900 84.96900 zmin,zma (A): -5.074000 68.23100 x,y,z range (A): 65.48600 66.57000 73.30499 scale (grids/A): 0.4856422 object centre (A): 47.17400 51.68400 31.57850 number of atom coordinates read : 5970 total number of charged atoms : 5800 net assigned charge : -2.985977 assigned positive charge : 898.5772 centred at (gu) : 90.31898 89.57074 90.88902 assigned negative charge : -901.5708 centred at (gu) : 90.30725 89.58842 91.02992 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8869 nv = 96 ne = 84 npr = 119803 no. pairs analyzed = 119803 no. exposed pairs = 7519 no. arc points = 51946 no. surface atoms = 2507 nbur = 3463 mkacc time = 0.2100000 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 = 1.764000 m= 301 mr = 4527 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3900000 number of dielectric boundary points 4639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4946 ## 808 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0571578E-10 -2.1168486E-10 midg,1,midg; midg,igrid,midg 8.0925535E-12 -2.7193942E-11 1,midg,midg; igrid,midg,midg -2.2199697E-11 9.1653800E-13 gauss-seidel spectral radius is 0.9784140 estimated iterations to convergence 56 setup time was (sec) 0.5800000 now iterating at: 08:58:39 rms-change max change #iterations 5.8817986E-02 8.170246 at 10iterations 3.3485058E-03 0.5351772 at 20iterations 5.2289345E-04 0.1264763 at 30iterations 1.4604483E-04 3.5379410E-02 at 40iterations 4.5278313E-05 1.0551453E-02 at 50iterations finished qdiffx linear iterations at : 08:58:42 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 4.5278313E-05 1.0551453E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 08:58:42 3.652u 0.175s 0:04.18 91.3% 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 08:58:43 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5970 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 1.456927 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): 14.43100 79.91700 ymin,ymax (A): 18.39900 84.96900 zmin,zma (A): -5.074000 68.23100 x,y,z range (A): 65.48600 66.57000 73.30499 scale (grids/A): 1.456927 object centre (A): 47.17400 51.68400 31.57850 number of atom coordinates read : 5970 total number of charged atoms : 5800 net assigned charge : -2.985977 assigned positive charge : 898.5772 centred at (gu) : 90.95525 88.71045 92.66525 assigned negative charge : -901.5708 centred at (gu) : 90.92151 88.76509 93.08947 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 100972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 28176 mr = 68958 m= 2049 mr = 18144 m= 30 mr = 669 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 754 time to turn everything in is 0.5000000 number of dielectric boundary points 43456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 806 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 42770 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) : 0.4856422 object centre at (A) : 47.17400 51.68400 31.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4264587E-02 -3.4861941E-02 midg,1,midg; midg,igrid,midg -1.1957375E-03 -1.1096990E-02 1,midg,midg; igrid,midg,midg 9.2598039E-04 -1.7667448E-03 gauss-seidel spectral radius is 0.9980056 estimated iterations to convergence 178 setup time was (sec) 0.7100000 now iterating at: 08:58:43 rms-change max change #iterations 3.865868 147.7094 at 10iterations 1.549706 47.31981 at 20iterations 0.6196300 23.60679 at 30iterations 0.2480572 7.929707 at 40iterations 9.9088326E-02 3.273933 at 50iterations 4.0152051E-02 1.230339 at 60iterations 1.6088272E-02 0.4926472 at 70iterations 6.5169530E-03 0.1990223 at 80iterations 2.6748667E-03 9.3054771E-02 at 90iterations 1.1300233E-03 4.5133591E-02 at 100iterations 5.0313171E-04 2.1316528E-02 at 110iterations 2.4817535E-04 1.1211395E-02 at 120iterations finished qdiffx linear iterations at : 08:58:51 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 2.4817535E-04 1.1211395E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 08:58:51 8.067u 0.207s 0:08.57 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 08:58:51 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5970 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.185390 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): 14.43100 79.91700 ymin,ymax (A): 18.39900 84.96900 zmin,zma (A): -5.074000 68.23100 x,y,z range (A): 65.48600 66.57000 73.30499 scale (grids/A): 2.185390 object centre (A): 47.17400 51.68400 31.57850 number of atom coordinates read : 5970 total number of charged atoms : 5800 net assigned charge : -2.985977 assigned positive charge : 898.5772 centred at (gu) : 91.43250 88.06520 93.99752 assigned negative charge : -901.5708 centred at (gu) : 91.38200 88.14737 94.63416 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 235485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 102684 mr = 169634 m= 23822 mr = 78943 m= 2628 mr = 16534 m= 86 mr = 1309 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 2719 time to turn everything in is 1.200000 number of dielectric boundary points 98277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 46137 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) : 1.456927 object centre at (A) : 47.17400 51.68400 31.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6751605 -0.9645387 midg,1,midg; midg,igrid,midg 8.7785451E-03 -0.2235419 1,midg,midg; igrid,midg,midg 3.0318892E-02 -8.1590258E-02 gauss-seidel spectral radius is 0.9991637 estimated iterations to convergence 273 setup time was (sec) 1.450000 now iterating at: 08:58:53 rms-change max change #iterations 10.85842 324.8185 at 10iterations 6.262214 164.7169 at 20iterations 3.584272 75.58986 at 30iterations 2.038135 49.37415 at 40iterations 1.156489 23.45153 at 50iterations 0.6536342 14.03000 at 60iterations 0.3683836 6.669783 at 70iterations 0.2074920 4.076960 at 80iterations 0.1167024 2.307592 at 90iterations 6.5410480E-02 1.134193 at 100iterations 3.6618274E-02 0.6796761 at 110iterations 2.0513266E-02 0.3752708 at 120iterations 1.1499685E-02 0.2077560 at 130iterations 6.4273472E-03 0.1151562 at 140iterations 3.6064698E-03 6.9529533E-02 at 150iterations 2.0189232E-03 3.5684586E-02 at 160iterations 1.1349177E-03 2.0515442E-02 at 170iterations 6.3996390E-04 1.2228012E-02 at 180iterations finished qdiffx linear iterations at : 08:59:05 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 6.3996390E-04 1.2228012E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 08:59:05 13.454u 0.207s 0:13.93 97.9% 0+0k 0+0io 0pf+0w