Wed Feb 15 08:54:22 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:22 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 = 2622 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: 0.5909891 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 0.5909891 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 387.1810 centred at (gu) : 89.97933 90.85722 89.57085 assigned negative charge : -387.1814 centred at (gu) : 89.79717 90.70245 89.63102 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6029 nv = 96 ne = 84 npr = 53468 no. pairs analyzed = 53468 no. exposed pairs = 3567 no. arc points = 24927 no. surface atoms = 1205 nbur = 1417 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 271 mr = 2989 m= 0 mr = 9 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2444 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7693945E-09 -1.5375259E-09 midg,1,midg; midg,igrid,midg -3.5693042E-09 5.0530096E-09 1,midg,midg; igrid,midg,midg -5.1664304E-09 4.8277689E-09 gauss-seidel spectral radius is 0.9851910 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 08:54:23 rms-change max change #iterations 9.9872902E-02 16.96946 at 10iterations 8.0652880E-03 1.210836 at 20iterations 6.6382246E-04 0.1200638 at 30iterations 5.4285425E-05 1.0560036E-02 at 40iterations 4.4581539E-06 6.8092346E-04 at 50iterations finished qdiffx linear iterations at : 08:54:26 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.4581539E-06 6.8092346E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 08:54:27 3.559u 0.200s 0:05.31 70.6% 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 Wed Feb 15 2012 at 08:54:28 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 = 2622 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: 1.772967 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 1.772967 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 387.1810 centred at (gu) : 89.93729 92.57142 88.71226 assigned negative charge : -387.1814 centred at (gu) : 89.39121 92.10690 88.89270 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 65756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24927 grid for indexing accessible points = 1.400000 m= 20975 mr = 43557 m= 2397 mr = 13970 m= 118 mr = 1080 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 30616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19251 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) : 0.5909891 object centre at (A) : 18.24750 43.24300 81.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8634890E-03 1.3723652E-03 midg,1,midg; midg,igrid,midg -6.5200212E-03 1.1982670E-02 1,midg,midg; igrid,midg,midg -2.3721443E-02 7.8308973E-03 gauss-seidel spectral radius is 0.9984345 estimated iterations to convergence 201 setup time was (sec) 0.5300000 now iterating at: 08:54:29 rms-change max change #iterations 3.678599 174.3349 at 10iterations 1.617128 60.47072 at 20iterations 0.7199835 27.97446 at 30iterations 0.3182730 12.80758 at 40iterations 0.1408592 5.008865 at 50iterations 6.2622987E-02 2.200335 at 60iterations 2.7819188E-02 0.9130592 at 70iterations 1.2327881E-02 0.4129295 at 80iterations 5.4778932E-03 0.2039537 at 90iterations 2.4313859E-03 0.1065674 at 100iterations 1.0783600E-03 4.0046692E-02 at 110iterations 4.7853589E-04 1.7698765E-02 at 120iterations finished qdiffx linear iterations at : 08:54:36 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 4.7853589E-04 1.7698765E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 08:54:36 8.064u 0.252s 0:08.66 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 Wed Feb 15 2012 at 08:54:37 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 = 2622 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: 2.659451 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 2.659451 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 387.1810 centred at (gu) : 89.90598 93.85683 88.06837 assigned negative charge : -387.1814 centred at (gu) : 89.08669 93.16031 88.33894 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 152133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24927 grid for indexing accessible points = 1.400000 m= 70596 mr = 106426 m= 21515 mr = 54938 m= 3644 mr = 15607 m= 346 mr = 2231 m= 14 mr = 162 m= 0 mr = 8 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 68876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19794 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) : 1.772967 object centre at (A) : 18.24750 43.24300 81.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2018226 2.0319931E-02 midg,1,midg; midg,igrid,midg -7.1904831E-02 3.1331889E-02 1,midg,midg; igrid,midg,midg -0.3055531 5.4553706E-02 gauss-seidel spectral radius is 0.9992131 estimated iterations to convergence 281 setup time was (sec) 1.190000 now iterating at: 08:54:39 rms-change max change #iterations 9.184769 317.0917 at 10iterations 5.382786 136.5935 at 20iterations 3.100546 71.78701 at 30iterations 1.782384 39.53973 at 40iterations 1.021022 22.69512 at 50iterations 0.5823431 13.36008 at 60iterations 0.3307888 8.823708 at 70iterations 0.1878770 4.105415 at 80iterations 0.1066067 2.271635 at 90iterations 6.0449395E-02 1.209192 at 100iterations 3.4266949E-02 0.6860123 at 110iterations 1.9352157E-02 0.4447970 at 120iterations 1.0946605E-02 0.2256660 at 130iterations 6.1962372E-03 0.1182022 at 140iterations 3.4953651E-03 6.3920975E-02 at 150iterations 1.9767552E-03 3.9556503E-02 at 160iterations 1.1136292E-03 2.2263527E-02 at 170iterations 6.2963174E-04 1.2477875E-02 at 180iterations finished qdiffx linear iterations at : 08:54:53 total time elapsed so far: 15.63000 # loops : 180 mean,max change (kT/e) : 6.2963174E-04 1.2477875E-02 energy calculations done at 15.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.75000 DelPhi exited at 08:54:56 15.753u 0.314s 0:18.66 86.0% 0+0k 0+0io 0pf+0w