Sat Oct 15 11:50:50 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 15 2011 at 11:50:50 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 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: 0.6556048 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): -26.73200 26.35700 ymin,ymax (A): 7.799000 50.18400 zmin,zma (A): -12.81100 41.49000 x,y,z range (A): 53.08900 42.38500 54.30100 scale (grids/A): 0.6556048 object centre (A): -0.1875000 28.99150 14.33950 number of atom coordinates read : 2354 total number of charged atoms : 2211 net assigned charge : 11.00002 assigned positive charge : 341.3573 centred at (gu) : 90.06998 90.54157 91.28207 assigned negative charge : -330.3581 centred at (gu) : 90.08823 90.49856 91.28467 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6902 nv = 96 ne = 84 npr = 47889 no. pairs analyzed = 47889 no. exposed pairs = 3048 no. arc points = 21726 no. surface atoms = 1023 nbur = 1331 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3646 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8042 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9431383E-08 3.1589526E-08 midg,1,midg; midg,igrid,midg 1.6401687E-08 3.4822357E-08 1,midg,midg; igrid,midg,midg 2.7083050E-08 2.2301448E-08 gauss-seidel spectral radius is 0.9879270 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 11:50:51 rms-change max change #iterations 0.1459827 28.65161 at 10iterations 1.5312434E-02 2.459892 at 20iterations 1.6576233E-03 0.2232857 at 30iterations 2.2812694E-04 3.7681580E-02 at 40iterations 5.8476231E-05 1.1605263E-02 at 50iterations finished qdiffx linear iterations at : 11:50:54 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.8476231E-05 1.1605263E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 11:50:54 3.322u 0.185s 0:03.98 87.9% 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 15 2011 at 11:50:54 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 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: 1.966815 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): -26.73200 26.35700 ymin,ymax (A): 7.799000 50.18400 zmin,zma (A): -12.81100 41.49000 x,y,z range (A): 53.08900 42.38500 54.30100 scale (grids/A): 1.966815 object centre (A): -0.1875000 28.99150 14.33950 number of atom coordinates read : 2354 total number of charged atoms : 2211 net assigned charge : 11.00002 assigned positive charge : 341.3573 centred at (gu) : 90.20942 91.62426 93.84571 assigned negative charge : -330.3581 centred at (gu) : 90.26450 91.49569 93.85406 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 27108 mr = 49901 m= 4864 mr = 19650 m= 362 mr = 2989 m= 7 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 33380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17427 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) : 0.6556048 object centre at (A) : -0.1875000 28.99150 14.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7855263E-02 2.7734753E-02 midg,1,midg; midg,igrid,midg 2.4801894E-04 2.4948070E-02 1,midg,midg; igrid,midg,midg 4.3281779E-02 5.2053787E-02 gauss-seidel spectral radius is 0.9986999 estimated iterations to convergence 220 setup time was (sec) 0.5700000 now iterating at: 11:50:55 rms-change max change #iterations 4.171484 186.8159 at 10iterations 1.984843 73.07021 at 20iterations 0.9433327 32.80426 at 30iterations 0.4519235 15.54484 at 40iterations 0.2148736 6.598289 at 50iterations 0.1021267 3.279282 at 60iterations 4.8659537E-02 1.571066 at 70iterations 2.3215838E-02 0.7232361 at 80iterations 1.1063516E-02 0.3707352 at 90iterations 5.2887863E-03 0.1630993 at 100iterations 2.5418238E-03 8.3938599E-02 at 110iterations 1.2270425E-03 4.1564941E-02 at 120iterations finished qdiffx linear iterations at : 11:51:02 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.2270425E-03 4.1564941E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 11:51:03 7.673u 0.194s 0:08.45 93.0% 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 Sat Oct 15 2011 at 11:51:03 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 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: 2.950222 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): -26.73200 26.35700 ymin,ymax (A): 7.799000 50.18400 zmin,zma (A): -12.81100 41.49000 x,y,z range (A): 53.08900 42.38500 54.30100 scale (grids/A): 2.950222 object centre (A): -0.1875000 28.99150 14.33950 number of atom coordinates read : 2354 total number of charged atoms : 2211 net assigned charge : 11.00002 assigned positive charge : 341.3573 centred at (gu) : 90.31419 92.43623 95.76852 assigned negative charge : -330.3581 centred at (gu) : 90.39675 92.24359 95.78104 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 170463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 85922 mr = 121366 m= 32695 mr = 69316 m= 9003 mr = 26079 m= 1542 mr = 6620 m= 99 mr = 1045 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 75268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 17688 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) : 1.966815 object centre at (A) : -0.1875000 28.99150 14.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7535203 0.3055978 midg,1,midg; midg,igrid,midg -3.4829207E-02 0.2316347 1,midg,midg; igrid,midg,midg 0.3826797 0.5131133 gauss-seidel spectral radius is 0.9992789 estimated iterations to convergence 294 setup time was (sec) 1.170000 now iterating at: 11:51:04 rms-change max change #iterations 9.709466 387.3314 at 10iterations 5.724003 138.2584 at 20iterations 3.357796 73.75279 at 30iterations 1.960038 47.58762 at 40iterations 1.148577 24.05020 at 50iterations 0.6704152 12.82879 at 60iterations 0.3906998 7.961398 at 70iterations 0.2272901 5.219131 at 80iterations 0.1321112 2.448931 at 90iterations 7.6668538E-02 1.414154 at 100iterations 4.4554755E-02 0.9397712 at 110iterations 2.5860401E-02 0.4618306 at 120iterations 1.5002612E-02 0.3045502 at 130iterations 8.7046223E-03 0.1979351 at 140iterations 5.0630695E-03 9.9821091E-02 at 150iterations 2.9385588E-03 5.1861525E-02 at 160iterations 1.7195181E-03 3.2232285E-02 at 170iterations 1.0140750E-03 2.0876884E-02 at 180iterations finished qdiffx linear iterations at : 11:51:15 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 1.0140750E-03 2.0876884E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 11:51:16 12.436u 0.218s 0:12.96 97.5% 0+0k 0+0io 0pf+0w