Tue Oct 11 03:36:57 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 03:36:57 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 0.6431914 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): -15.65200 27.39700 ymin,ymax (A): -3.151000 51.24700 zmin,zma (A): -5.250000 50.09900 x,y,z range (A): 43.04900 54.39800 55.34900 scale (grids/A): 0.6431914 object centre (A): 5.872500 24.04800 22.42450 number of atom coordinates read : 2227 total number of charged atoms : 2122 net assigned charge : -6.485982 assigned positive charge : 329.1654 centred at (gu) : 88.91014 89.54663 90.20114 assigned negative charge : -335.6518 centred at (gu) : 88.74216 89.70352 90.21323 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6268 nv = 96 ne = 84 npr = 45922 no. pairs analyzed = 45922 no. exposed pairs = 2807 no. arc points = 19980 no. surface atoms = 959 nbur = 1268 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3376 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2600000 number of dielectric boundary points 3186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1895 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7412 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4788043E-09 -1.1977662E-08 midg,1,midg; midg,igrid,midg 7.5498541E-09 -2.5148470E-08 1,midg,midg; igrid,midg,midg -3.6588979E-08 6.1910694E-09 gauss-seidel spectral radius is 0.9874467 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 03:36:57 rms-change max change #iterations 0.1383963 22.79551 at 10iterations 1.4153567E-02 2.023521 at 20iterations 1.4248837E-03 0.2030907 at 30iterations 1.4147309E-04 1.9140244E-02 at 40iterations 1.4056266E-05 2.3250580E-03 at 50iterations finished qdiffx linear iterations at : 03:37:00 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.4056266E-05 2.3250580E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 03:37:01 3.217u 0.174s 0:04.00 84.5% 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 03:37:01 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 1.929574 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): -15.65200 27.39700 ymin,ymax (A): -3.151000 51.24700 zmin,zma (A): -5.250000 50.09900 x,y,z range (A): 43.04900 54.39800 55.34900 scale (grids/A): 1.929574 object centre (A): 5.872500 24.04800 22.42450 number of atom coordinates read : 2227 total number of charged atoms : 2122 net assigned charge : -6.485982 assigned positive charge : 329.1654 centred at (gu) : 86.73012 88.63956 90.60336 assigned negative charge : -335.6518 centred at (gu) : 86.22641 89.11038 90.63963 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19980 grid for indexing accessible points = 1.400000 m= 23599 mr = 45536 m= 3809 mr = 17186 m= 222 mr = 2326 m= 6 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 156 time to turn everything in is 0.4800000 number of dielectric boundary points 29361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 16708 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) : 0.6431914 object centre at (A) : 5.872500 24.04800 22.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5555945E-03 -3.5899911E-02 midg,1,midg; midg,igrid,midg -4.9043126E-02 -6.6792287E-02 1,midg,midg; igrid,midg,midg -1.7499186E-02 1.7750302E-02 gauss-seidel spectral radius is 0.9986350 estimated iterations to convergence 214 setup time was (sec) 0.7600000 now iterating at: 03:37:02 rms-change max change #iterations 4.030679 222.8420 at 10iterations 1.881377 69.73454 at 20iterations 0.8823726 29.84969 at 30iterations 0.4126540 14.56710 at 40iterations 0.1930581 6.148087 at 50iterations 9.0046786E-02 3.099828 at 60iterations 4.2276543E-02 1.468668 at 70iterations 1.9722050E-02 0.6393204 at 80iterations 9.2542786E-03 0.2972794 at 90iterations 4.3177879E-03 0.1570015 at 100iterations 2.0288501E-03 6.9952965E-02 at 110iterations 9.4968767E-04 3.3035278E-02 at 120iterations finished qdiffx linear iterations at : 03:37:08 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 9.4968767E-04 3.3035278E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 03:37:08 7.009u 0.181s 0:07.48 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 Tue Oct 11 2011 at 03:37:08 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 2.894361 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): -15.65200 27.39700 ymin,ymax (A): -3.151000 51.24700 zmin,zma (A): -5.250000 50.09900 x,y,z range (A): 43.04900 54.39800 55.34900 scale (grids/A): 2.894361 object centre (A): 5.872500 24.04800 22.42450 number of atom coordinates read : 2227 total number of charged atoms : 2122 net assigned charge : -6.485982 assigned positive charge : 329.1654 centred at (gu) : 85.09510 87.95946 90.90478 assigned negative charge : -335.6518 centred at (gu) : 84.33958 88.66560 90.95948 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 154596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19980 grid for indexing accessible points = 1.400000 m= 76038 mr = 110755 m= 28159 mr = 61577 m= 6861 mr = 22436 m= 961 mr = 5018 m= 60 mr = 626 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 548 time to turn everything in is 1.180000 number of dielectric boundary points 66238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 16976 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) : 1.929574 object centre at (A) : 5.872500 24.04800 22.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6206790E-02 -0.3372858 midg,1,midg; midg,igrid,midg -0.4852887 -0.9277894 1,midg,midg; igrid,midg,midg -0.1375990 0.1935860 gauss-seidel spectral radius is 0.9992571 estimated iterations to convergence 290 setup time was (sec) 1.470000 now iterating at: 03:37:10 rms-change max change #iterations 9.310492 346.1492 at 10iterations 5.386941 124.4689 at 20iterations 3.101255 64.95754 at 30iterations 1.782145 34.45118 at 40iterations 1.022873 20.50093 at 50iterations 0.5872306 12.83540 at 60iterations 0.3371269 6.206299 at 70iterations 0.1932872 3.831656 at 80iterations 0.1108237 1.995486 at 90iterations 6.3352026E-02 1.354410 at 100iterations 3.6261450E-02 0.6528263 at 110iterations 2.0832649E-02 0.3833733 at 120iterations 1.1932024E-02 0.2473602 at 130iterations 6.8213800E-03 0.1473699 at 140iterations 3.9046833E-03 8.0676079E-02 at 150iterations 2.2364967E-03 4.2657614E-02 at 160iterations 1.2789746E-03 2.3942471E-02 at 170iterations 7.3448318E-04 1.5520096E-02 at 180iterations finished qdiffx linear iterations at : 03:37:20 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 7.3448318E-04 1.5520096E-02 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 03:37:21 11.587u 0.209s 0:12.26 96.0% 0+0k 0+0io 0pf+0w