Tue Oct 11 04:19:54 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 04:19:54 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6628929 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): -14.72000 29.59000 ymin,ymax (A): 7.576000 51.81300 zmin,zma (A): 25.83300 79.53699 x,y,z range (A): 44.31000 44.23700 53.70399 scale (grids/A): 0.6628929 object centre (A): 7.435000 29.69450 52.68500 number of atom coordinates read : 2543 total number of charged atoms : 2394 net assigned charge : 4.176023 assigned positive charge : 382.7179 centred at (gu) : 90.64149 90.89852 88.93853 assigned negative charge : -378.5426 centred at (gu) : 90.96243 90.64100 89.06863 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7501 nv = 96 ne = 84 npr = 52430 no. pairs analyzed = 52430 no. exposed pairs = 3083 no. arc points = 21207 no. surface atoms = 1041 nbur = 1502 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4331 m= 1 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3400000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2021 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8785 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7324239E-08 -1.2736560E-08 midg,1,midg; midg,igrid,midg -3.5973962E-08 7.6420733E-08 1,midg,midg; igrid,midg,midg 6.6156005E-08 -6.6108903E-08 gauss-seidel spectral radius is 0.9881971 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 04:19:55 rms-change max change #iterations 0.1733915 27.98142 at 10iterations 1.9077474E-02 2.432786 at 20iterations 2.1570118E-03 0.2640991 at 30iterations 3.1260130E-04 4.1046143E-02 at 40iterations 6.9455127E-05 9.0179443E-03 at 50iterations finished qdiffx linear iterations at : 04:19:58 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 6.9455127E-05 9.0179443E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 04:19:58 3.589u 0.138s 0:04.08 90.9% 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 Tue Oct 11 2011 at 04:19:58 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.988679 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): -14.72000 29.59000 ymin,ymax (A): 7.576000 51.81300 zmin,zma (A): 25.83300 79.53699 x,y,z range (A): 44.31000 44.23700 53.70399 scale (grids/A): 1.988679 object centre (A): 7.435000 29.69450 52.68500 number of atom coordinates read : 2543 total number of charged atoms : 2394 net assigned charge : 4.176023 assigned positive charge : 382.7179 centred at (gu) : 91.92411 92.69524 86.81529 assigned negative charge : -378.5426 centred at (gu) : 92.88701 91.92301 87.20596 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21207 grid for indexing accessible points = 1.400000 m= 31257 mr = 57881 m= 5320 mr = 23558 m= 360 mr = 3501 m= 8 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1302 time to turn everything in is 0.6200000 number of dielectric boundary points 32982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18915 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) : 0.6628929 object centre at (A) : 7.435000 29.69450 52.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7272534E-02 -2.3990527E-02 midg,1,midg; midg,igrid,midg -1.3826379E-02 5.6452960E-02 1,midg,midg; igrid,midg,midg 6.2042590E-02 -5.0965946E-02 gauss-seidel spectral radius is 0.9987364 estimated iterations to convergence 223 setup time was (sec) 0.9000000 now iterating at: 04:19:59 rms-change max change #iterations 4.581687 200.2178 at 10iterations 2.216254 69.62966 at 20iterations 1.066207 35.49400 at 30iterations 0.5151017 16.82348 at 40iterations 0.2488732 8.140644 at 50iterations 0.1198905 3.547642 at 60iterations 5.8091398E-02 1.794892 at 70iterations 2.8053343E-02 0.8637085 at 80iterations 1.3545785E-02 0.4040527 at 90iterations 6.5411092E-03 0.2110901 at 100iterations 3.1862985E-03 0.1026955 at 110iterations 1.5468436E-03 4.8210144E-02 at 120iterations finished qdiffx linear iterations at : 04:20:06 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.5468436E-03 4.8210144E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 04:20:06 7.546u 0.170s 0:07.99 96.4% 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 04:20:06 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.983018 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): -14.72000 29.59000 ymin,ymax (A): 7.576000 51.81300 zmin,zma (A): 25.83300 79.53699 x,y,z range (A): 44.31000 44.23700 53.70399 scale (grids/A): 2.983018 object centre (A): 7.435000 29.69450 52.68500 number of atom coordinates read : 2543 total number of charged atoms : 2394 net assigned charge : 4.176023 assigned positive charge : 382.7179 centred at (gu) : 92.88594 94.04273 85.22277 assigned negative charge : -378.5426 centred at (gu) : 94.33044 92.88448 85.80873 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 187354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21207 grid for indexing accessible points = 1.400000 m= 99178 mr = 139393 m= 38065 mr = 82607 m= 9736 mr = 31084 m= 1601 mr = 7456 m= 117 mr = 1105 m= 2 mr = 61 m= 0 mr = 2 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4593 time to turn everything in is 1.600000 number of dielectric boundary points 74345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 19140 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) : 1.988679 object centre at (A) : 7.435000 29.69450 52.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5345886 -0.1093963 midg,1,midg; midg,igrid,midg -0.1410072 0.4712966 1,midg,midg; igrid,midg,midg 0.5282451 -0.5648644 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.910000 now iterating at: 04:20:08 rms-change max change #iterations 10.50570 367.9850 at 10iterations 6.181635 148.2469 at 20iterations 3.627956 64.96655 at 30iterations 2.126511 43.44385 at 40iterations 1.242717 28.53177 at 50iterations 0.7246748 13.83642 at 60iterations 0.4218439 7.401430 at 70iterations 0.2456269 4.485509 at 80iterations 0.1431514 2.472269 at 90iterations 8.3227418E-02 1.513512 at 100iterations 4.8435375E-02 0.8880901 at 110iterations 2.8164314E-02 0.4893951 at 120iterations 1.6409550E-02 0.2872925 at 130iterations 9.5870057E-03 0.1700115 at 140iterations 5.6056012E-03 0.1045609 at 150iterations 3.3161303E-03 6.1029911E-02 at 160iterations 1.9935903E-03 3.7654877E-02 at 170iterations 1.2240027E-03 2.2093058E-02 at 180iterations finished qdiffx linear iterations at : 04:20:18 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 1.2240027E-03 2.2093058E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 04:20:19 12.188u 0.195s 0:12.72 97.2% 0+0k 0+0io 0pf+0w