Sun Oct 9 17:23:36 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 Sun Oct 9 2011 at 17:23:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5141 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5480380 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): 3.225000 68.18400 ymin,ymax (A): -8.537000 53.47000 zmin,zma (A): -1.226000 62.04800 x,y,z range (A): 64.95900 62.00700 63.27400 scale (grids/A): 0.5480380 object centre (A): 35.70450 22.46650 30.41100 number of atom coordinates read : 5141 total number of charged atoms : 4990 net assigned charge : -0.3789496 assigned positive charge : 787.8746 centred at (gu) : 87.90162 89.15239 89.28560 assigned negative charge : -788.2596 centred at (gu) : 87.77963 89.18201 89.27283 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10005 nv = 96 ne = 84 npr = 104495 no. pairs analyzed = 104495 no. exposed pairs = 6119 no. arc points = 41235 no. surface atoms = 2082 nbur = 3059 mkacc time = 0.2500000 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= 431 mr = 5641 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4188 ## 487 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13212 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8180321E-10 1.4227987E-10 midg,1,midg; midg,igrid,midg 4.7344406E-10 -2.9646033E-10 1,midg,midg; igrid,midg,midg -2.6505984E-09 9.0745039E-10 gauss-seidel spectral radius is 0.9829869 estimated iterations to convergence 63 setup time was (sec) 0.7600000 now iterating at: 17:23:37 rms-change max change #iterations 0.1045019 13.78076 at 10iterations 9.5571335E-03 1.253616 at 20iterations 2.8828015E-03 0.3420563 at 30iterations 1.3709818E-03 0.1502609 at 40iterations 6.7922345E-04 7.8074932E-02 at 50iterations finished qdiffx linear iterations at : 17:23:39 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 6.7922345E-04 7.8074932E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:23:40 3.560u 0.136s 0:03.96 93.1% 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 17:23:40 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5141 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.644114 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): 3.225000 68.18400 ymin,ymax (A): -8.537000 53.47000 zmin,zma (A): -1.226000 62.04800 x,y,z range (A): 64.95900 62.00700 63.27400 scale (grids/A): 1.644114 object centre (A): 35.70450 22.46650 30.41100 number of atom coordinates read : 5141 total number of charged atoms : 4990 net assigned charge : -0.3789496 assigned positive charge : 787.8746 centred at (gu) : 83.70346 87.45585 87.85522 assigned negative charge : -788.2596 centred at (gu) : 83.33891 87.54612 87.81854 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 111525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38414 mr = 80419 m= 4553 mr = 27572 m= 141 mr = 2384 m= 0 mr = 5 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 44253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 38271 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) : 0.5480380 object centre at (A) : 35.70450 22.46650 30.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9441940E-02 -1.7375804E-02 midg,1,midg; midg,igrid,midg 1.6476959E-02 8.2813390E-03 1,midg,midg; igrid,midg,midg -3.0718790E-02 1.4183237E-02 gauss-seidel spectral radius is 0.9984057 estimated iterations to convergence 199 setup time was (sec) 1.080000 now iterating at: 17:23:41 rms-change max change #iterations 4.709475 178.1069 at 10iterations 2.071395 57.91331 at 20iterations 0.9166154 27.26294 at 30iterations 0.4036903 10.81796 at 40iterations 0.1791646 5.032883 at 50iterations 7.9393141E-02 2.266421 at 60iterations 3.5590671E-02 0.9428878 at 70iterations 1.6286837E-02 0.4791021 at 80iterations 8.0034649E-03 0.2339439 at 90iterations 4.4154236E-03 0.1134987 at 100iterations 2.8011973E-03 7.3982239E-02 at 110iterations 1.9926638E-03 4.9495697E-02 at 120iterations finished qdiffx linear iterations at : 17:23:47 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.9926638E-03 4.9495697E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 17:23:48 7.810u 0.183s 0:08.26 96.7% 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 Sun Oct 9 2011 at 17:23:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5141 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.466171 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): 3.225000 68.18400 ymin,ymax (A): -8.537000 53.47000 zmin,zma (A): -1.226000 62.04800 x,y,z range (A): 64.95900 62.00700 63.27400 scale (grids/A): 2.466171 object centre (A): 35.70450 22.46650 30.41100 number of atom coordinates read : 5141 total number of charged atoms : 4990 net assigned charge : -0.3789496 assigned positive charge : 787.8746 centred at (gu) : 80.55489 86.18332 86.78248 assigned negative charge : -788.2596 centred at (gu) : 80.00833 86.31905 86.72792 start vw surface at 0.2200000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 259301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41235 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 129688 mr = 195920 m= 40738 mr = 105190 m= 7405 mr = 31455 m= 588 mr = 5033 m= 13 mr = 254 m= 0 mr = 2 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 99879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 39874 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) : 1.644114 object centre at (A) : 35.70450 22.46650 30.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3546780 -0.4026055 midg,1,midg; midg,igrid,midg 7.8608923E-02 -6.4350492E-03 1,midg,midg; igrid,midg,midg -0.5148145 0.1834312 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 2.320000 now iterating at: 17:23:50 rms-change max change #iterations 12.05149 350.7253 at 10iterations 7.091915 141.0426 at 20iterations 4.138462 84.36590 at 30iterations 2.412837 51.07904 at 40iterations 1.397138 24.58917 at 50iterations 0.8085877 13.74994 at 60iterations 0.4672004 7.817070 at 70iterations 0.2693785 4.629517 at 80iterations 0.1552499 2.500693 at 90iterations 8.9401066E-02 1.455681 at 100iterations 5.1669013E-02 0.8220825 at 110iterations 2.9899480E-02 0.5480213 at 120iterations 1.7577706E-02 0.2774200 at 130iterations 1.0554066E-02 0.1781535 at 140iterations 6.6176001E-03 0.1087799 at 150iterations 4.3972461E-03 7.8678131E-02 at 160iterations 3.1501618E-03 4.9007535E-02 at 170iterations 2.4185691E-03 3.6846280E-02 at 180iterations finished qdiffx linear iterations at : 17:24:01 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 2.4185691E-03 3.6846280E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 17:24:01 13.046u 0.179s 0:13.49 97.9% 0+0k 0+0io 0pf+0w