Sun Oct 9 13:47:48 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 13:47:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7116868 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): -1.181000 45.48700 ymin,ymax (A): 36.39100 86.41300 zmin,zma (A): -24.52200 24.79700 x,y,z range (A): 46.66800 50.02200 49.31900 scale (grids/A): 0.7116868 object centre (A): 22.15300 61.40200 0.1374998 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 90.03729 89.93652 91.67027 assigned negative charge : -356.4896 centred at (gu) : 90.17646 90.03331 91.60477 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8241 nv = 96 ne = 84 npr = 47391 no. pairs analyzed = 47391 no. exposed pairs = 2978 no. arc points = 20870 no. surface atoms = 999 nbur = 1367 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4632 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1849 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8947 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9736962E-09 1.0004353E-07 midg,1,midg; midg,igrid,midg 9.2398167E-08 -2.8259135E-08 1,midg,midg; igrid,midg,midg 1.1605132E-07 -5.5937505E-08 gauss-seidel spectral radius is 0.9897397 estimated iterations to convergence 80 setup time was (sec) 0.3800000 now iterating at: 13:47:48 rms-change max change #iterations 0.2225325 28.11458 at 10iterations 2.8241647E-02 3.541405 at 20iterations 4.0547010E-03 0.5097408 at 30iterations 8.6777593E-04 0.1451530 at 40iterations 2.7691430E-04 4.5169830E-02 at 50iterations finished qdiffx linear iterations at : 13:47:51 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.7691430E-04 4.5169830E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:47:52 3.416u 0.176s 0:03.89 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 13:47:52 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 = 2366 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: 2.135061 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): -1.181000 45.48700 ymin,ymax (A): 36.39100 86.41300 zmin,zma (A): -24.52200 24.79700 x,y,z range (A): 46.66800 50.02200 49.31900 scale (grids/A): 2.135061 object centre (A): 22.15300 61.40200 0.1374998 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 90.11154 89.80929 95.01039 assigned negative charge : -356.4896 centred at (gu) : 90.52918 90.09968 94.81422 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20870 grid for indexing accessible points = 1.400000 m= 33860 mr = 60613 m= 6244 mr = 25345 m= 558 mr = 3996 m= 15 mr = 273 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17675 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) : 0.7116868 object centre at (A) : 22.15300 61.40200 0.1374998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6590308E-02 2.9434573E-02 midg,1,midg; midg,igrid,midg 0.1058633 3.0945559E-04 1,midg,midg; igrid,midg,midg 2.0455807E-03 -1.7848801E-02 gauss-seidel spectral radius is 0.9988802 estimated iterations to convergence 236 setup time was (sec) 0.6600000 now iterating at: 13:47:52 rms-change max change #iterations 5.028168 205.3791 at 10iterations 2.519721 99.66277 at 20iterations 1.260581 36.76772 at 30iterations 0.6373286 23.72582 at 40iterations 0.3203539 9.243969 at 50iterations 0.1616230 4.832768 at 60iterations 8.1305042E-02 2.400330 at 70iterations 4.1189529E-02 1.367142 at 80iterations 2.0867666E-02 0.5907841 at 90iterations 1.0707915E-02 0.2995033 at 100iterations 5.5170762E-03 0.1626587 at 110iterations 2.9149491E-03 9.1659546E-02 at 120iterations finished qdiffx linear iterations at : 13:48:00 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.9149491E-03 9.1659546E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:48:00 7.984u 0.192s 0:08.45 96.6% 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 13:48:00 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 = 2366 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: 3.202591 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): -1.181000 45.48700 ymin,ymax (A): 36.39100 86.41300 zmin,zma (A): -24.52200 24.79700 x,y,z range (A): 46.66800 50.02200 49.31900 scale (grids/A): 3.202591 object centre (A): 22.15300 61.40200 0.1374998 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 90.16710 89.71381 97.51548 assigned negative charge : -356.4896 centred at (gu) : 90.79367 90.14938 97.22129 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 199770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20870 grid for indexing accessible points = 1.400000 m= 106239 mr = 145851 m= 42204 mr = 87807 m= 11606 mr = 34176 m= 2317 mr = 8831 m= 278 mr = 1659 m= 10 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 83923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 17800 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) : 2.135061 object centre at (A) : 22.15300 61.40200 0.1374998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3215405 0.4315986 midg,1,midg; midg,igrid,midg 1.450497 -0.1410722 1,midg,midg; igrid,midg,midg -2.0548038E-02 -0.1440171 gauss-seidel spectral radius is 0.9993138 estimated iterations to convergence 301 setup time was (sec) 1.590000 now iterating at: 13:48:02 rms-change max change #iterations 11.23580 387.7194 at 10iterations 6.719543 156.3858 at 20iterations 4.009664 86.10985 at 30iterations 2.387813 44.55154 at 40iterations 1.416339 26.43759 at 50iterations 0.8389196 16.69353 at 60iterations 0.4958729 8.578690 at 70iterations 0.2941924 5.014191 at 80iterations 0.1732219 3.068375 at 90iterations 0.1024427 1.790328 at 100iterations 6.0553335E-02 1.095846 at 110iterations 3.5949312E-02 0.6173782 at 120iterations 2.1476120E-02 0.3876038 at 130iterations 1.3034410E-02 0.2251511 at 140iterations 8.1027960E-03 0.1489258 at 150iterations 5.2683107E-03 0.1173630 at 160iterations 3.6170229E-03 7.8342438E-02 at 170iterations 2.6530402E-03 5.7716370E-02 at 180iterations finished qdiffx linear iterations at : 13:48:13 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 2.6530402E-03 5.7716370E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 13:48:14 13.200u 0.195s 0:13.71 97.6% 0+0k 0+0io 0pf+0w