Sun Oct 9 00:53:51 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+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 00:53:51 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 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: 0.6479914 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): 0.2590001 53.83100 ymin,ymax (A): -15.56600 27.60900 zmin,zma (A): 30.06100 85.00000 x,y,z range (A): 53.57200 43.17500 54.93900 scale (grids/A): 0.6479914 object centre (A): 27.04500 6.021501 57.53050 number of atom coordinates read : 2325 total number of charged atoms : 2190 net assigned charge : 10.00002 assigned positive charge : 339.7574 centred at (gu) : 90.15161 89.17065 88.93927 assigned negative charge : -329.7581 centred at (gu) : 90.15475 89.29523 88.91648 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6764 nv = 96 ne = 84 npr = 45920 no. pairs analyzed = 45920 no. exposed pairs = 3158 no. arc points = 22855 no. surface atoms = 1050 nbur = 1275 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3510 m= 0 mr = 38 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7839 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9017055E-08 1.6848727E-08 midg,1,midg; midg,igrid,midg 3.9556582E-08 2.3583788E-09 1,midg,midg; igrid,midg,midg 1.7957101E-08 1.8307141E-08 gauss-seidel spectral radius is 0.9876441 estimated iterations to convergence 74 setup time was (sec) 0.5000000 now iterating at: 00:53:52 rms-change max change #iterations 0.1452104 20.82066 at 10iterations 1.4697370E-02 2.654381 at 20iterations 1.5334055E-03 0.2308712 at 30iterations 1.8001467E-04 2.7334690E-02 at 40iterations 2.8954111E-05 3.8757324E-03 at 50iterations finished qdiffx linear iterations at : 00:53:54 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 2.8954111E-05 3.8757324E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 00:53:55 3.286u 0.189s 0:03.76 92.0% 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 00:53:55 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 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: 1.943974 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): 0.2590001 53.83100 ymin,ymax (A): -15.56600 27.60900 zmin,zma (A): 30.06100 85.00000 x,y,z range (A): 53.57200 43.17500 54.93900 scale (grids/A): 1.943974 object centre (A): 27.04500 6.021501 57.53050 number of atom coordinates read : 2325 total number of charged atoms : 2190 net assigned charge : 10.00002 assigned positive charge : 339.7574 centred at (gu) : 90.45457 87.51164 86.81730 assigned negative charge : -329.7581 centred at (gu) : 90.46439 87.88592 86.74951 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22855 grid for indexing accessible points = 1.400000 m= 25976 mr = 47645 m= 4528 mr = 18542 m= 350 mr = 2776 m= 4 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 206 time to turn everything in is 0.5300000 number of dielectric boundary points 33546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17265 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) : 0.6479914 object centre at (A) : 27.04500 6.021501 57.53050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9661848E-02 4.0173739E-02 midg,1,midg; midg,igrid,midg 3.2155115E-02 -7.7401386E-03 1,midg,midg; igrid,midg,midg 5.3020276E-02 5.6631956E-02 gauss-seidel spectral radius is 0.9986718 estimated iterations to convergence 217 setup time was (sec) 0.8200000 now iterating at: 00:53:56 rms-change max change #iterations 4.044764 181.9448 at 10iterations 1.912848 68.15010 at 20iterations 0.8996388 31.18816 at 30iterations 0.4271144 15.16923 at 40iterations 0.2014579 6.619313 at 50iterations 9.4832852E-02 2.824956 at 60iterations 4.4697996E-02 1.421935 at 70iterations 2.1235365E-02 0.6734810 at 80iterations 1.0037255E-02 0.3426952 at 90iterations 4.7751516E-03 0.1557236 at 100iterations 2.2628522E-03 7.5504303E-02 at 110iterations 1.0824491E-03 3.4144402E-02 at 120iterations finished qdiffx linear iterations at : 00:54:03 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 1.0824491E-03 3.4144402E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 00:54:03 7.624u 0.216s 0:08.17 95.8% 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 00:54:03 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 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: 2.915961 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): 0.2590001 53.83100 ymin,ymax (A): -15.56600 27.60900 zmin,zma (A): 30.06100 85.00000 x,y,z range (A): 53.57200 43.17500 54.93900 scale (grids/A): 2.915961 object centre (A): 27.04500 6.021501 57.53050 number of atom coordinates read : 2325 total number of charged atoms : 2190 net assigned charge : 10.00002 assigned positive charge : 339.7574 centred at (gu) : 90.68186 86.26739 85.22610 assigned negative charge : -329.7581 centred at (gu) : 90.69659 86.82898 85.12431 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 165607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22855 grid for indexing accessible points = 1.400000 m= 82357 mr = 116028 m= 31285 mr = 65670 m= 8366 mr = 24714 m= 1374 mr = 6133 m= 117 mr = 913 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 668 time to turn everything in is 1.310000 number of dielectric boundary points 75588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 17520 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) : 1.943974 object centre at (A) : 27.04500 6.021501 57.53050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2490399 0.4988967 midg,1,midg; midg,igrid,midg 0.2890521 -8.8197485E-02 1,midg,midg; igrid,midg,midg 0.6456701 0.5462812 gauss-seidel spectral radius is 0.9992770 estimated iterations to convergence 293 setup time was (sec) 1.620000 now iterating at: 00:54:05 rms-change max change #iterations 9.633237 377.5126 at 10iterations 5.711493 138.5943 at 20iterations 3.359193 71.38544 at 30iterations 1.968431 39.25025 at 40iterations 1.150698 22.26268 at 50iterations 0.6701878 13.36654 at 60iterations 0.3907378 7.514598 at 70iterations 0.2270947 4.677315 at 80iterations 0.1322789 2.629494 at 90iterations 7.6667778E-02 1.488582 at 100iterations 4.4517171E-02 0.8674030 at 110iterations 2.5878077E-02 0.4725895 at 120iterations 1.4985292E-02 0.2782593 at 130iterations 8.6652655E-03 0.1574829 at 140iterations 5.0300960E-03 9.5219612E-02 at 150iterations 2.9164657E-03 5.4085732E-02 at 160iterations 1.6923324E-03 2.9983521E-02 at 170iterations 9.8527875E-04 2.0436525E-02 at 180iterations finished qdiffx linear iterations at : 00:54:16 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 9.8527875E-04 2.0436525E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 00:54:16 12.437u 0.250s 0:12.95 97.9% 0+0k 0+0io 0pf+0w