Sat Oct 8 16:15:28 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+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 Sat Oct 8 2011 at 16:15:28 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 = 2454 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6233912 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): -2.370000 45.05700 ymin,ymax (A): -15.34400 29.72900 zmin,zma (A): -18.82600 38.28100 x,y,z range (A): 47.42700 45.07300 57.10700 scale (grids/A): 0.6233912 object centre (A): 21.34350 7.192500 9.727501 number of atom coordinates read : 2454 total number of charged atoms : 2389 net assigned charge : 1.500002 assigned positive charge : 367.1949 centred at (gu) : 91.14067 88.72215 90.01929 assigned negative charge : -365.6958 centred at (gu) : 91.23745 88.86502 90.12748 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 48815 no. pairs analyzed = 48815 no. exposed pairs = 3153 no. arc points = 22071 no. surface atoms = 1065 nbur = 1389 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3501 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2186 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6218739E-09 -6.2750338E-09 midg,1,midg; midg,igrid,midg 1.4616083E-08 -6.5404508E-09 1,midg,midg; igrid,midg,midg 6.1408869E-09 -7.0620700E-09 gauss-seidel spectral radius is 0.9866630 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 16:15:28 rms-change max change #iterations 0.1229936 17.75019 at 10iterations 1.1596066E-02 1.613604 at 20iterations 1.0858629E-03 0.1708221 at 30iterations 1.0889518E-04 1.6964912E-02 at 40iterations 1.4509335E-05 2.0370483E-03 at 50iterations finished qdiffx linear iterations at : 16:15:31 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 1.4509335E-05 2.0370483E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 16:15:31 3.138u 0.189s 0:03.62 91.4% 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 Sat Oct 8 2011 at 16:15:31 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 = 2454 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: 1.870173 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): -2.370000 45.05700 ymin,ymax (A): -15.34400 29.72900 zmin,zma (A): -18.82600 38.28100 x,y,z range (A): 47.42700 45.07300 57.10700 scale (grids/A): 1.870173 object centre (A): 21.34350 7.192500 9.727501 number of atom coordinates read : 2454 total number of charged atoms : 2389 net assigned charge : 1.500002 assigned positive charge : 367.1949 centred at (gu) : 93.42150 86.16550 90.05729 assigned negative charge : -365.6958 centred at (gu) : 93.71214 86.59482 90.38243 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22071 grid for indexing accessible points = 1.400000 m= 23995 mr = 48540 m= 3586 mr = 17405 m= 181 mr = 2242 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 732 time to turn everything in is 0.4900000 number of dielectric boundary points 29675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 18755 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) : 0.6233912 object centre at (A) : 21.34350 7.192500 9.727501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6171111E-02 -1.6884496E-02 midg,1,midg; midg,igrid,midg 2.1663427E-02 -6.1101243E-03 1,midg,midg; igrid,midg,midg 6.5846941E-03 -3.8724925E-02 gauss-seidel spectral radius is 0.9985743 estimated iterations to convergence 210 setup time was (sec) 0.7600000 now iterating at: 16:15:32 rms-change max change #iterations 3.969604 169.6401 at 10iterations 1.816427 62.06910 at 20iterations 0.8424283 32.89891 at 30iterations 0.3888003 13.43543 at 40iterations 0.1793947 6.430168 at 50iterations 8.2534894E-02 2.552795 at 60iterations 3.8071033E-02 1.290108 at 70iterations 1.7617382E-02 0.6144943 at 80iterations 8.1219897E-03 0.2480087 at 90iterations 3.7500125E-03 0.1186724 at 100iterations 1.7291558E-03 5.5992126E-02 at 110iterations 7.9839153E-04 2.7725697E-02 at 120iterations finished qdiffx linear iterations at : 16:15:40 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 7.9839153E-04 2.7725697E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 16:15:40 8.231u 0.229s 0:08.81 95.9% 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 Sat Oct 8 2011 at 16:15:40 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 = 2454 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.805260 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): -2.370000 45.05700 ymin,ymax (A): -15.34400 29.72900 zmin,zma (A): -18.82600 38.28100 x,y,z range (A): 47.42700 45.07300 57.10700 scale (grids/A): 2.805260 object centre (A): 21.34350 7.192500 9.727501 number of atom coordinates read : 2454 total number of charged atoms : 2389 net assigned charge : 1.500002 assigned positive charge : 367.1949 centred at (gu) : 95.13223 84.24822 90.08579 assigned negative charge : -365.6958 centred at (gu) : 95.56819 84.89226 90.57372 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 162326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22071 grid for indexing accessible points = 1.400000 m= 78963 mr = 118150 m= 27518 mr = 63702 m= 6537 mr = 22036 m= 817 mr = 4874 m= 43 mr = 520 m= 0 mr = 18 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2280 time to turn everything in is 1.240000 number of dielectric boundary points 66904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19109 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) : 1.870173 object centre at (A) : 21.34350 7.192500 9.727501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1640573 -0.2500672 midg,1,midg; midg,igrid,midg 0.1974293 -8.5569844E-02 1,midg,midg; igrid,midg,midg 6.5937787E-02 -0.5153118 gauss-seidel spectral radius is 0.9992420 estimated iterations to convergence 287 setup time was (sec) 1.550000 now iterating at: 16:15:42 rms-change max change #iterations 9.434138 367.7310 at 10iterations 5.501946 146.3024 at 20iterations 3.187228 71.91951 at 30iterations 1.846001 46.18760 at 40iterations 1.062966 22.24364 at 50iterations 0.6108612 12.58658 at 60iterations 0.3510141 7.725159 at 70iterations 0.2011326 3.729882 at 80iterations 0.1152027 2.178725 at 90iterations 6.5916471E-02 1.229786 at 100iterations 3.7734009E-02 0.7648029 at 110iterations 2.1536624E-02 0.4166479 at 120iterations 1.2318300E-02 0.2386360 at 130iterations 7.0446823E-03 0.1333675 at 140iterations 4.0251603E-03 7.5471878E-02 at 150iterations 2.2987532E-03 4.4893503E-02 at 160iterations 1.3123818E-03 2.4443626E-02 at 170iterations 7.4963184E-04 1.5117645E-02 at 180iterations finished qdiffx linear iterations at : 16:15:52 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 7.4963184E-04 1.5117645E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 16:15:53 12.022u 0.232s 0:12.57 97.4% 0+0k 0+0io 0pf+0w