Sat Oct 8 11:45:31 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 Sat Oct 8 2011 at 11:45:31 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 448 has a net charge of 0.5140 !!! WARNING: HIR 454 has a net charge of 0.5140 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: 0.6265289 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): 15.89400 72.71500 ymin,ymax (A): 13.00700 63.90900 zmin,zma (A): 21.30200 64.63400 x,y,z range (A): 56.82100 50.90200 43.33200 scale (grids/A): 0.6265289 object centre (A): 44.30450 38.45800 42.96800 number of atom coordinates read : 2586 total number of charged atoms : 2446 net assigned charge : -1.957991 assigned positive charge : 402.4711 centred at (gu) : 91.53580 91.15466 91.39615 assigned negative charge : -404.4294 centred at (gu) : 91.57748 91.05573 91.43023 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6578 nv = 96 ne = 84 npr = 52733 no. pairs analyzed = 52733 no. exposed pairs = 3156 no. arc points = 22899 no. surface atoms = 1063 nbur = 1523 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3493 m= 5 mr = 48 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 0.3400000 number of dielectric boundary points 3400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2300 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4866895E-10 -6.4490617E-09 midg,1,midg; midg,igrid,midg -7.9316038E-09 8.0880840E-09 1,midg,midg; igrid,midg,midg 1.0731467E-09 -7.5506756E-09 gauss-seidel spectral radius is 0.9868040 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 11:45:32 rms-change max change #iterations 0.1385795 21.67366 at 10iterations 1.2860439E-02 1.912235 at 20iterations 1.2136383E-03 0.1754303 at 30iterations 1.1269076E-04 1.6820908E-02 at 40iterations 1.0681055E-05 1.4648438E-03 at 50iterations finished qdiffx linear iterations at : 11:45:35 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.0681055E-05 1.4648438E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 11:45:36 4.130u 0.278s 0:04.67 94.2% 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 11:45:36 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 448 has a net charge of 0.5140 !!! WARNING: HIR 454 has a net charge of 0.5140 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: 1.879587 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): 15.89400 72.71500 ymin,ymax (A): 13.00700 63.90900 zmin,zma (A): 21.30200 64.63400 x,y,z range (A): 56.82100 50.90200 43.33200 scale (grids/A): 1.879587 object centre (A): 44.30450 38.45800 42.96800 number of atom coordinates read : 2586 total number of charged atoms : 2446 net assigned charge : -1.957991 assigned positive charge : 402.4711 centred at (gu) : 94.60723 93.46359 94.18785 assigned negative charge : -404.4294 centred at (gu) : 94.73219 93.16685 94.29072 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22899 grid for indexing accessible points = 1.400000 m= 24100 mr = 48598 m= 3503 mr = 17368 m= 211 mr = 2124 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 0.6400000 number of dielectric boundary points 31426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19183 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) : 0.6265289 object centre at (A) : 44.30450 38.45800 42.96800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4310926E-04 -1.8901752E-02 midg,1,midg; midg,igrid,midg -1.0359233E-02 -1.1152554E-03 1,midg,midg; igrid,midg,midg 1.4714148E-02 -3.3227440E-02 gauss-seidel spectral radius is 0.9985969 estimated iterations to convergence 212 setup time was (sec) 0.9400000 now iterating at: 11:45:37 rms-change max change #iterations 4.265385 211.1333 at 10iterations 1.971721 74.25574 at 20iterations 0.9087343 30.62761 at 30iterations 0.4210646 15.11085 at 40iterations 0.1948445 6.714389 at 50iterations 9.0156548E-02 2.868406 at 60iterations 4.1693728E-02 1.375580 at 70iterations 1.9364584E-02 0.6675228 at 80iterations 8.9772157E-03 0.3267841 at 90iterations 4.1553085E-03 0.1238708 at 100iterations 1.9217767E-03 6.1518192E-02 at 110iterations 8.9185929E-04 3.1440735E-02 at 120iterations finished qdiffx linear iterations at : 11:45:46 total time elapsed so far: 9.400000 # loops : 120 mean,max change (kT/e) : 8.9185929E-04 3.1440735E-02 energy calculations done at 9.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 11:45:46 9.586u 0.302s 0:10.15 97.3% 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 11:45:46 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 448 has a net charge of 0.5140 !!! WARNING: HIR 454 has a net charge of 0.5140 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: 2.819380 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): 15.89400 72.71500 ymin,ymax (A): 13.00700 63.90900 zmin,zma (A): 21.30200 64.63400 x,y,z range (A): 56.82100 50.90200 43.33200 scale (grids/A): 2.819380 object centre (A): 44.30450 38.45800 42.96800 number of atom coordinates read : 2586 total number of charged atoms : 2446 net assigned charge : -1.957991 assigned positive charge : 402.4711 centred at (gu) : 96.91077 95.19529 96.28173 assigned negative charge : -404.4294 centred at (gu) : 97.09824 94.75030 96.43596 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22899 grid for indexing accessible points = 1.400000 m= 79240 mr = 118334 m= 27098 mr = 63902 m= 6215 mr = 21420 m= 882 mr = 4632 m= 67 mr = 604 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2658 time to turn everything in is 1.610000 number of dielectric boundary points 70771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 19568 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) : 1.879587 object centre at (A) : 44.30450 38.45800 42.96800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2569409E-02 -0.3328370 midg,1,midg; midg,igrid,midg -9.8694228E-02 -8.3451740E-02 1,midg,midg; igrid,midg,midg 0.2439944 -0.2444178 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.940000 now iterating at: 11:45:48 rms-change max change #iterations 9.968958 347.9845 at 10iterations 5.786510 121.0532 at 20iterations 3.324325 68.08515 at 30iterations 1.900920 37.24942 at 40iterations 1.087225 19.64478 at 50iterations 0.6210393 11.60828 at 60iterations 0.3556727 7.131068 at 70iterations 0.2024984 4.140715 at 80iterations 0.1154988 2.075550 at 90iterations 6.6048935E-02 1.219473 at 100iterations 3.7708506E-02 0.7941384 at 110iterations 2.1543656E-02 0.4071102 at 120iterations 1.2289275E-02 0.2419310 at 130iterations 7.0034061E-03 0.1363745 at 140iterations 3.9980365E-03 7.7072144E-02 at 150iterations 2.2844605E-03 3.9263248E-02 at 160iterations 1.3047707E-03 2.4799347E-02 at 170iterations 7.4545352E-04 1.3931274E-02 at 180iterations finished qdiffx linear iterations at : 11:46:02 total time elapsed so far: 15.77000 # loops : 180 mean,max change (kT/e) : 7.4545352E-04 1.3931274E-02 energy calculations done at 15.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 11:46:03 15.946u 0.311s 0:16.52 98.3% 0+0k 0+0io 0pf+0w