Tue Oct 11 06:43:21 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 06:43:21 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 = 2089 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: 0.7108341 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): -19.66000 24.78500 ymin,ymax (A): -13.01900 28.00800 zmin,zma (A): -3.560000 46.52200 x,y,z range (A): 44.44500 41.02700 50.08200 scale (grids/A): 0.7108341 object centre (A): 2.562500 7.494501 21.48100 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.73981 90.07011 90.64633 assigned negative charge : -311.0742 centred at (gu) : 89.61046 90.07704 90.71902 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6843 nv = 96 ne = 84 npr = 43719 no. pairs analyzed = 43719 no. exposed pairs = 2351 no. arc points = 16048 no. surface atoms = 803 nbur = 1286 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 3960 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.2800000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1494 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6885443E-08 2.3394652E-08 midg,1,midg; midg,igrid,midg 6.2790775E-08 5.6991063E-08 1,midg,midg; igrid,midg,midg -1.0417383E-08 1.2155328E-07 gauss-seidel spectral radius is 0.9896756 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 06:43:22 rms-change max change #iterations 0.2060626 28.58241 at 10iterations 2.5619570E-02 3.664631 at 20iterations 3.2045476E-03 0.4189606 at 30iterations 4.0636578E-04 6.0049057E-02 at 40iterations 5.4341544E-05 9.3288422E-03 at 50iterations finished qdiffx linear iterations at : 06:43:24 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 5.4341544E-05 9.3288422E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:43:25 3.299u 0.135s 0:03.86 88.6% 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 Tue Oct 11 2011 at 06:43:25 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 = 2089 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: 2.132503 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): -19.66000 24.78500 ymin,ymax (A): -13.01900 28.00800 zmin,zma (A): -3.560000 46.52200 x,y,z range (A): 44.44500 41.02700 50.08200 scale (grids/A): 2.132503 object centre (A): 2.562500 7.494501 21.48100 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.21949 90.21038 91.93893 assigned negative charge : -311.0742 centred at (gu) : 88.83168 90.23142 92.15720 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16048 grid for indexing accessible points = 1.400000 m= 26893 mr = 52243 m= 4838 mr = 20003 m= 453 mr = 3111 m= 16 mr = 237 m= 0 mr = 6 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2614 time to turn everything in is 0.5600000 number of dielectric boundary points 29451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15575 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) : 0.7108341 object centre at (A) : 2.562500 7.494501 21.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7207754E-02 6.5100648E-02 midg,1,midg; midg,igrid,midg 2.4625223E-02 8.6889360E-03 1,midg,midg; igrid,midg,midg 1.4147357E-02 3.6457848E-02 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.8400000 now iterating at: 06:43:26 rms-change max change #iterations 4.623477 170.5435 at 10iterations 2.289604 81.03399 at 20iterations 1.131155 36.21068 at 30iterations 0.5648740 16.25240 at 40iterations 0.2794717 8.342760 at 50iterations 0.1389130 4.218061 at 60iterations 6.8972066E-02 2.086015 at 70iterations 3.4242075E-02 1.098858 at 80iterations 1.6998500E-02 0.4986267 at 90iterations 8.4356181E-03 0.2848129 at 100iterations 4.1845809E-03 0.1223803 at 110iterations 2.0868832E-03 6.6909790E-02 at 120iterations finished qdiffx linear iterations at : 06:43:32 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.0868832E-03 6.6909790E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 06:43:33 7.456u 0.170s 0:08.24 92.4% 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 06:43:33 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 = 2089 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: 3.198754 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): -19.66000 24.78500 ymin,ymax (A): -13.01900 28.00800 zmin,zma (A): -3.560000 46.52200 x,y,z range (A): 44.44500 41.02700 50.08200 scale (grids/A): 3.198754 object centre (A): 2.562500 7.494501 21.48100 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 88.82913 90.31555 92.90829 assigned negative charge : -311.0742 centred at (gu) : 88.24747 90.34713 93.23579 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 168766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16048 grid for indexing accessible points = 1.400000 m= 86577 mr = 126411 m= 32667 mr = 71633 m= 9069 mr = 26420 m= 1795 mr = 6825 m= 197 mr = 1301 m= 10 mr = 120 m= 0 mr = 7 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 8489 time to turn everything in is 1.770000 number of dielectric boundary points 66364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 15688 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) : 2.132503 object centre at (A) : 2.562500 7.494501 21.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3167357 0.6754139 midg,1,midg; midg,igrid,midg 0.1992867 5.1247198E-02 1,midg,midg; igrid,midg,midg 0.2787747 0.3497540 gauss-seidel spectral radius is 0.9992895 estimated iterations to convergence 296 setup time was (sec) 2.050000 now iterating at: 06:43:35 rms-change max change #iterations 10.21681 387.0798 at 10iterations 6.032498 162.1698 at 20iterations 3.550746 95.51876 at 30iterations 2.088791 46.22814 at 40iterations 1.224126 23.07257 at 50iterations 0.7164183 12.74548 at 60iterations 0.4197829 7.986370 at 70iterations 0.2453103 4.645920 at 80iterations 0.1431283 2.933158 at 90iterations 8.3530165E-02 1.531653 at 100iterations 4.8765797E-02 0.8193436 at 110iterations 2.8503478E-02 0.4663429 at 120iterations 1.6695816E-02 0.3145828 at 130iterations 9.7599365E-03 0.1723938 at 140iterations 5.7369629E-03 9.6202850E-02 at 150iterations 3.3880293E-03 6.4941406E-02 at 160iterations 2.0261109E-03 3.6586761E-02 at 170iterations 1.2337146E-03 2.3334503E-02 at 180iterations finished qdiffx linear iterations at : 06:43:46 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 1.2337146E-03 2.3334503E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 06:43:46 12.305u 0.198s 0:13.05 95.7% 0+0k 0+0io 0pf+0w