Sun Oct 9 11:53:28 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 11:53:29 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1884 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: 0.7364502 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): 8.183001 56.52300 ymin,ymax (A): -19.38100 28.80600 zmin,zma (A): 94.24400 132.5350 x,y,z range (A): 48.34000 48.18700 38.29099 scale (grids/A): 0.7364502 object centre (A): 32.35300 4.712500 113.3895 number of atom coordinates read : 1884 total number of charged atoms : 1808 net assigned charge : 2.000006 assigned positive charge : 275.2861 centred at (gu) : 89.28365 90.73923 89.99913 assigned negative charge : -273.2864 centred at (gu) : 89.04870 90.66675 90.01503 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7609 nv = 96 ne = 84 npr = 36310 no. pairs analyzed = 36310 no. exposed pairs = 2664 no. arc points = 18760 no. surface atoms = 910 nbur = 974 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 660 mr = 4084 m= 3 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 7.9999983E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6718561E-08 2.1079863E-08 midg,1,midg; midg,igrid,midg -2.1363356E-08 1.0574195E-07 1,midg,midg; igrid,midg,midg -1.8394233E-07 1.9116983E-07 gauss-seidel spectral radius is 0.9903855 estimated iterations to convergence 83 setup time was (sec) 0.4900000 now iterating at: 11:53:29 rms-change max change #iterations 0.2239979 28.91038 at 10iterations 2.9424246E-02 4.145013 at 20iterations 3.8975012E-03 0.4979019 at 30iterations 5.1737041E-04 6.5986633E-02 at 40iterations 6.9763591E-05 9.1297626E-03 at 50iterations finished qdiffx linear iterations at : 11:53:32 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.9763591E-05 9.1297626E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 11:53:32 3.439u 0.220s 0:03.94 92.6% 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 Sun Oct 9 2011 at 11:53:33 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1884 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: 2.209351 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): 8.183001 56.52300 ymin,ymax (A): -19.38100 28.80600 zmin,zma (A): 94.24400 132.5350 x,y,z range (A): 48.34000 48.18700 38.29099 scale (grids/A): 2.209351 object centre (A): 32.35300 4.712500 113.3895 number of atom coordinates read : 1884 total number of charged atoms : 1808 net assigned charge : 2.000006 assigned positive charge : 275.2861 centred at (gu) : 87.85085 92.21774 89.99781 assigned negative charge : -273.2864 centred at (gu) : 87.14635 92.00056 90.04522 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18760 grid for indexing accessible points = 1.400000 m= 34038 mr = 52541 m= 9266 mr = 25844 m= 1306 mr = 6819 m= 60 mr = 797 m= 0 mr = 19 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14410 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) : 0.7364502 object centre at (A) : 32.35300 4.712500 113.3895 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6895932E-02 2.6938543E-02 midg,1,midg; midg,igrid,midg -1.3682139E-02 1.4949279E-02 1,midg,midg; igrid,midg,midg -3.6341902E-02 4.4917990E-02 gauss-seidel spectral radius is 0.9989178 estimated iterations to convergence 240 setup time was (sec) 0.9100000 now iterating at: 11:53:34 rms-change max change #iterations 4.706562 214.9242 at 10iterations 2.384420 79.86541 at 20iterations 1.207257 37.85088 at 30iterations 0.6142119 19.47771 at 40iterations 0.3124483 9.456076 at 50iterations 0.1585598 4.355604 at 60iterations 8.0727868E-02 2.539366 at 70iterations 4.0977933E-02 1.281044 at 80iterations 2.0827396E-02 0.6252060 at 90iterations 1.0594498E-02 0.3280640 at 100iterations 5.3911461E-03 0.1567080 at 110iterations 2.7467979E-03 8.3849430E-02 at 120iterations finished qdiffx linear iterations at : 11:53:41 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.7467979E-03 8.3849430E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 11:53:41 7.991u 0.271s 0:08.54 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 11:53:41 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1884 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: 3.314026 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): 8.183001 56.52300 ymin,ymax (A): -19.38100 28.80600 zmin,zma (A): 94.24400 132.5350 x,y,z range (A): 48.34000 48.18700 38.29099 scale (grids/A): 3.314026 object centre (A): 32.35300 4.712500 113.3895 number of atom coordinates read : 1884 total number of charged atoms : 1808 net assigned charge : 2.000006 assigned positive charge : 275.2861 centred at (gu) : 86.77637 93.32673 89.99673 assigned negative charge : -273.2864 centred at (gu) : 85.71957 93.00099 90.06786 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18760 grid for indexing accessible points = 1.400000 m= 99049 mr = 126434 m= 48828 mr = 81438 m= 18673 mr = 40947 m= 5099 mr = 15395 m= 821 mr = 4068 m= 48 mr = 607 m= 0 mr = 23 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 82876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 14463 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) : 2.209351 object centre at (A) : 32.35300 4.712500 113.3895 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4385408 0.2745205 midg,1,midg; midg,igrid,midg -0.1959551 0.6182841 1,midg,midg; igrid,midg,midg -0.1907651 0.3829338 gauss-seidel spectral radius is 0.9993361 estimated iterations to convergence 306 setup time was (sec) 2.250000 now iterating at: 11:53:44 rms-change max change #iterations 10.30004 323.3344 at 10iterations 6.183170 145.0391 at 20iterations 3.703064 82.77995 at 30iterations 2.212225 45.75724 at 40iterations 1.322791 27.04801 at 50iterations 0.7890753 13.74463 at 60iterations 0.4699970 9.469475 at 70iterations 0.2795384 5.068750 at 80iterations 0.1659084 3.309284 at 90iterations 9.8579988E-02 1.634805 at 100iterations 5.8377281E-02 0.9449158 at 110iterations 3.4668449E-02 0.5713860 at 120iterations 2.0539498E-02 0.3311481 at 130iterations 1.2184358E-02 0.2015190 at 140iterations 7.2198440E-03 0.1211557 at 150iterations 4.2755473E-03 7.1189880E-02 at 160iterations 2.5327916E-03 4.2095184E-02 at 170iterations 1.5007615E-03 2.4532080E-02 at 180iterations finished qdiffx linear iterations at : 11:53:57 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 1.5007615E-03 2.4532080E-02 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 11:53:58 15.901u 0.266s 0:16.45 98.2% 0+0k 0+0io 0pf+0w