Tue Oct 11 06:16:55 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 Tue Oct 11 2011 at 06:16:55 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2009 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7230923 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): -19.71200 24.11100 ymin,ymax (A): -9.988999 28.64600 zmin,zma (A): -3.488000 45.74500 x,y,z range (A): 43.82300 38.63500 49.23300 scale (grids/A): 0.7230923 object centre (A): 2.199500 9.328501 21.12850 number of atom coordinates read : 2009 total number of charged atoms : 1879 net assigned charge : 6.025006 assigned positive charge : 306.2732 centred at (gu) : 89.94010 89.06716 91.23799 assigned negative charge : -300.2481 centred at (gu) : 89.78271 89.10725 91.30760 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 39634 no. pairs analyzed = 39634 no. exposed pairs = 2551 no. arc points = 17526 no. surface atoms = 859 nbur = 1150 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4142 m= 1 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1523 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4870188E-08 3.2569496E-08 midg,1,midg; midg,igrid,midg 1.1932866E-07 3.9473157E-08 1,midg,midg; igrid,midg,midg -3.3831846E-08 1.7497270E-07 gauss-seidel spectral radius is 0.9900233 estimated iterations to convergence 81 setup time was (sec) 0.6400000 now iterating at: 06:16:56 rms-change max change #iterations 0.2158349 40.36003 at 10iterations 2.8328203E-02 3.654400 at 20iterations 3.7830959E-03 0.5474243 at 30iterations 6.0886837E-04 8.3622456E-02 at 40iterations 1.4118664E-04 1.9325256E-02 at 50iterations finished qdiffx linear iterations at : 06:16:59 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 1.4118664E-04 1.9325256E-02 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 06:17:00 4.407u 0.447s 0:05.37 90.1% 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 Oct 11 2011 at 06:17:00 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2009 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.169277 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): -19.71200 24.11100 ymin,ymax (A): -9.988999 28.64600 zmin,zma (A): -3.488000 45.74500 x,y,z range (A): 43.82300 38.63500 49.23300 scale (grids/A): 2.169277 object centre (A): 2.199500 9.328501 21.12850 number of atom coordinates read : 2009 total number of charged atoms : 1879 net assigned charge : 6.025006 assigned positive charge : 306.2732 centred at (gu) : 89.82056 87.20167 93.71402 assigned negative charge : -300.2481 centred at (gu) : 89.34827 87.32194 93.92282 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17526 grid for indexing accessible points = 1.400000 m= 32011 mr = 53772 m= 6924 mr = 24292 m= 724 mr = 4713 m= 20 mr = 372 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 32989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14930 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) : 0.7230923 object centre at (A) : 2.199500 9.328501 21.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2376122E-02 1.1376074E-02 midg,1,midg; midg,igrid,midg 4.0524930E-02 5.1357024E-03 1,midg,midg; igrid,midg,midg 2.6074627E-02 5.0107256E-02 gauss-seidel spectral radius is 0.9988714 estimated iterations to convergence 236 setup time was (sec) 1.150000 now iterating at: 06:17:02 rms-change max change #iterations 4.734988 190.7516 at 10iterations 2.374922 72.21429 at 20iterations 1.197051 35.85971 at 30iterations 0.6018286 18.20139 at 40iterations 0.3030528 9.721592 at 50iterations 0.1522839 4.925911 at 60iterations 7.6642580E-02 2.412666 at 70iterations 3.8624790E-02 1.136337 at 80iterations 1.9410811E-02 0.5682216 at 90iterations 9.8117990E-03 0.2761993 at 100iterations 4.9651214E-03 0.1504991 at 110iterations 2.5441006E-03 7.3581696E-02 at 120iterations finished qdiffx linear iterations at : 06:17:11 total time elapsed so far: 10.14000 # loops : 120 mean,max change (kT/e) : 2.5441006E-03 7.3581696E-02 energy calculations done at 10.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.34000 DelPhi exited at 06:17:12 10.347u 0.464s 0:11.44 94.4% 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 Tue Oct 11 2011 at 06:17:12 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2009 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.253915 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): -19.71200 24.11100 ymin,ymax (A): -9.988999 28.64600 zmin,zma (A): -3.488000 45.74500 x,y,z range (A): 43.82300 38.63500 49.23300 scale (grids/A): 3.253915 object centre (A): 2.199500 9.328501 21.12850 number of atom coordinates read : 2009 total number of charged atoms : 1879 net assigned charge : 6.025006 assigned positive charge : 306.2732 centred at (gu) : 89.73080 85.80239 95.57100 assigned negative charge : -300.2481 centred at (gu) : 89.02245 85.98289 95.88428 start vw surface at 0.1400000 fill in re-entrant regions at 1.010000 boundary points on vw surface= 175946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17526 grid for indexing accessible points = 1.400000 m= 97480 mr = 129500 m= 42133 mr = 80833 m= 13322 mr = 34855 m= 2918 mr = 10365 m= 388 mr = 2097 m= 13 mr = 250 m= 0 mr = 4 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.540000 number of dielectric boundary points 74296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.690000 number of grid points assigned charge 15024 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) : 2.169277 object centre at (A) : 2.199500 9.328501 21.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6409295E-02 2.1901891E-02 midg,1,midg; midg,igrid,midg 0.3244650 2.0150013E-02 1,midg,midg; igrid,midg,midg 0.4408588 0.4163359 gauss-seidel spectral radius is 0.9993075 estimated iterations to convergence 300 setup time was (sec) 2.910000 now iterating at: 06:17:15 rms-change max change #iterations 10.47330 317.0656 at 10iterations 6.271133 138.3695 at 20iterations 3.730944 93.12695 at 30iterations 2.219127 43.16642 at 40iterations 1.315668 27.91881 at 50iterations 0.7779647 13.78089 at 60iterations 0.4597201 8.500454 at 70iterations 0.2712090 5.461642 at 80iterations 0.1598048 2.842741 at 90iterations 9.4159141E-02 1.707279 at 100iterations 5.5588771E-02 0.9840946 at 110iterations 3.2905329E-02 0.5670700 at 120iterations 1.9522388E-02 0.3410759 at 130iterations 1.1744398E-02 0.2184448 at 140iterations 7.1957516E-03 0.1235085 at 150iterations 4.5511541E-03 7.6860428E-02 at 160iterations 3.0076411E-03 5.2066803E-02 at 170iterations 2.1096817E-03 3.7876129E-02 at 180iterations finished qdiffx linear iterations at : 06:17:30 total time elapsed so far: 18.01000 # loops : 180 mean,max change (kT/e) : 2.1096817E-03 3.7876129E-02 energy calculations done at 18.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.22000 DelPhi exited at 06:17:31 18.228u 0.481s 0:19.01 98.3% 0+0k 0+0io 0pf+0w