Tue Nov 22 14:12:20 PST 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 Tue Nov 22 2011 at 14:12:24 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6255271 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): -35.31800 10.55900 ymin,ymax (A): 1.090000 42.62000 zmin,zma (A): -0.2760000 56.63600 x,y,z range (A): 45.87700 41.53000 56.91200 scale (grids/A): 0.6255271 object centre (A): -12.37950 21.85500 28.18000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 291.0719 centred at (gu) : 90.29696 89.18895 89.83846 assigned negative charge : -286.0722 centred at (gu) : 90.24840 89.27138 89.85509 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5238 nv = 96 ne = 84 npr = 40209 no. pairs analyzed = 40209 no. exposed pairs = 2411 no. arc points = 16960 no. surface atoms = 821 nbur = 1145 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 261 mr = 2899 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1695 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8576233E-09 3.6248340E-09 midg,1,midg; midg,igrid,midg 1.1213849E-08 -2.2717640E-11 1,midg,midg; igrid,midg,midg 1.7951887E-09 7.9750002E-09 gauss-seidel spectral radius is 0.9867083 estimated iterations to convergence 71 setup time was (sec) 0.4400000 now iterating at: 14:12:28 rms-change max change #iterations 0.1123123 18.81058 at 10iterations 1.0588333E-02 1.848732 at 20iterations 9.6525671E-04 0.1453629 at 30iterations 9.3922150E-05 1.7358780E-02 at 40iterations 8.6106384E-06 1.3217926E-03 at 50iterations finished qdiffx linear iterations at : 14:12:36 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 8.6106384E-06 1.3217926E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 14:12:40 3.243u 0.163s 0:17.90 18.9% 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 Nov 22 2011 at 14:12:44 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.876581 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): -35.31800 10.55900 ymin,ymax (A): 1.090000 42.62000 zmin,zma (A): -0.2760000 56.63600 x,y,z range (A): 45.87700 41.53000 56.91200 scale (grids/A): 1.876581 object centre (A): -12.37950 21.85500 28.18000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 291.0719 centred at (gu) : 90.89087 87.56674 89.51541 assigned negative charge : -286.0722 centred at (gu) : 90.74537 87.81438 89.56544 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 56262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 20816 mr = 38857 m= 3358 mr = 15799 m= 182 mr = 2187 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.4000000 number of dielectric boundary points 23691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14369 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) : 0.6255271 object centre at (A) : -12.37950 21.85500 28.18000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4765154E-02 3.2213509E-02 midg,1,midg; midg,igrid,midg 4.6810210E-03 1.5508255E-03 1,midg,midg; igrid,midg,midg -1.6209948E-03 -3.6900020E-03 gauss-seidel spectral radius is 0.9985198 estimated iterations to convergence 206 setup time was (sec) 0.6700000 now iterating at: 14:12:49 rms-change max change #iterations 3.496943 168.1331 at 10iterations 1.592978 62.99704 at 20iterations 0.7192196 27.23104 at 30iterations 0.3272533 11.77889 at 40iterations 0.1485594 5.698944 at 50iterations 6.7181982E-02 2.347885 at 60iterations 3.0618569E-02 1.064077 at 70iterations 1.3826914E-02 0.5182915 at 80iterations 6.2972568E-03 0.2143574 at 90iterations 2.8514382E-03 0.1030750 at 100iterations 1.2974710E-03 4.6894073E-02 at 110iterations 5.8477034E-04 2.4417877E-02 at 120iterations finished qdiffx linear iterations at : 14:13:08 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 5.8477034E-04 2.4417877E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 14:13:11 7.234u 0.173s 0:27.85 26.5% 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 Nov 22 2011 at 14:13:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.814872 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): -35.31800 10.55900 ymin,ymax (A): 1.090000 42.62000 zmin,zma (A): -0.2760000 56.63600 x,y,z range (A): 45.87700 41.53000 56.91200 scale (grids/A): 2.814872 object centre (A): -12.37950 21.85500 28.18000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 291.0719 centred at (gu) : 91.33617 86.35002 89.27309 assigned negative charge : -286.0722 centred at (gu) : 91.11812 86.72169 89.34824 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 130034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 66971 mr = 93943 m= 25136 mr = 55516 m= 5887 mr = 20784 m= 712 mr = 4560 m= 66 mr = 518 m= 0 mr = 44 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 511 time to turn everything in is 0.9900000 number of dielectric boundary points 53441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 14672 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) : 1.876581 object centre at (A) : -12.37950 21.85500 28.18000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1076066 0.2210021 midg,1,midg; midg,igrid,midg -3.9191235E-02 9.5097926E-03 1,midg,midg; igrid,midg,midg -5.0280120E-02 -8.2171455E-02 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 1.290000 now iterating at: 14:13:20 rms-change max change #iterations 8.348951 352.6925 at 10iterations 4.786918 119.7659 at 20iterations 2.710755 64.32183 at 30iterations 1.537648 36.55789 at 40iterations 0.8718117 17.32726 at 50iterations 0.4906181 11.72795 at 60iterations 0.2766347 5.945513 at 70iterations 0.1563786 3.267115 at 80iterations 8.8114940E-02 1.848218 at 90iterations 4.9690872E-02 1.029888 at 100iterations 2.7990960E-02 0.6023979 at 110iterations 1.5751010E-02 0.3492709 at 120iterations 8.8907378E-03 0.1891556 at 130iterations 4.9990164E-03 0.1029148 at 140iterations 2.8194017E-03 5.8994293E-02 at 150iterations 1.5841260E-03 3.4233093E-02 at 160iterations 8.9248008E-04 1.8260956E-02 at 170iterations 5.0333794E-04 9.8705292E-03 at 180iterations finished qdiffx linear iterations at : 14:13:52 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 5.0333794E-04 9.8705292E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 14:14:03 11.979u 0.189s 0:51.11 23.7% 0+0k 0+0io 0pf+0w