Tue Oct 11 08:16:45 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 08:16:45 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6632264 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): -24.93300 21.51800 ymin,ymax (A): -64.18200 -10.50500 zmin,zma (A): -17.28900 29.93100 x,y,z range (A): 46.45100 53.67700 47.22000 scale (grids/A): 0.6632264 object centre (A): -1.707500 -37.34350 6.321000 number of atom coordinates read : 2741 total number of charged atoms : 2606 net assigned charge : 3.000016 assigned positive charge : 420.0883 centred at (gu) : 90.71275 89.93626 90.60397 assigned negative charge : -417.0894 centred at (gu) : 90.55647 90.20372 90.65236 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8177 nv = 96 ne = 84 npr = 56655 no. pairs analyzed = 56655 no. exposed pairs = 3376 no. arc points = 22912 no. surface atoms = 1136 nbur = 1605 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4706 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2000000 number of dielectric boundary points 3880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2110 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7041438E-08 -3.5308705E-09 midg,1,midg; midg,igrid,midg 6.9121143E-08 -5.4584941E-08 1,midg,midg; igrid,midg,midg -2.4457210E-08 5.0715656E-08 gauss-seidel spectral radius is 0.9882284 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 08:16:45 rms-change max change #iterations 0.1805999 27.67107 at 10iterations 2.0018499E-02 2.770378 at 20iterations 3.1776610E-03 0.6116486 at 30iterations 9.3853299E-04 0.1930923 at 40iterations 3.4306172E-04 7.1128845E-02 at 50iterations finished qdiffx linear iterations at : 08:16:48 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.4306172E-04 7.1128845E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:16:48 3.338u 0.176s 0:03.90 89.7% 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 08:16:49 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.989679 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): -24.93300 21.51800 ymin,ymax (A): -64.18200 -10.50500 zmin,zma (A): -17.28900 29.93100 x,y,z range (A): 46.45100 53.67700 47.22000 scale (grids/A): 1.989679 object centre (A): -1.707500 -37.34350 6.321000 number of atom coordinates read : 2741 total number of charged atoms : 2606 net assigned charge : 3.000016 assigned positive charge : 420.0883 centred at (gu) : 92.13747 89.80800 91.81082 assigned negative charge : -417.0894 centred at (gu) : 91.66898 90.61105 91.95683 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 88244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22912 grid for indexing accessible points = 1.400000 m= 33393 mr = 62974 m= 5800 mr = 25154 m= 438 mr = 3792 m= 4 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1440 time to turn everything in is 0.4200000 number of dielectric boundary points 35778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20588 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) : 0.6632264 object centre at (A) : -1.707500 -37.34350 6.321000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7068604E-02 -2.7608272E-02 midg,1,midg; midg,igrid,midg 7.4211188E-02 -6.1055206E-02 1,midg,midg; igrid,midg,midg -1.6496204E-02 5.2642312E-02 gauss-seidel spectral radius is 0.9987603 estimated iterations to convergence 225 setup time was (sec) 0.6400000 now iterating at: 08:16:49 rms-change max change #iterations 4.825487 286.3796 at 10iterations 2.350818 68.81532 at 20iterations 1.137223 35.24109 at 30iterations 0.5515732 16.43986 at 40iterations 0.2690416 7.912607 at 50iterations 0.1303322 3.567857 at 60iterations 6.3708305E-02 1.814306 at 70iterations 3.1253237E-02 1.012695 at 80iterations 1.5493541E-02 0.4388580 at 90iterations 7.8800200E-03 0.2466965 at 100iterations 4.1842465E-03 0.1349792 at 110iterations 2.3715957E-03 9.2582703E-02 at 120iterations finished qdiffx linear iterations at : 08:16:56 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.3715957E-03 9.2582703E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:16:57 7.773u 0.179s 0:08.61 92.2% 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 Tue Oct 11 2011 at 08:16:57 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.984519 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): -24.93300 21.51800 ymin,ymax (A): -64.18200 -10.50500 zmin,zma (A): -17.28900 29.93100 x,y,z range (A): 46.45100 53.67700 47.22000 scale (grids/A): 2.984519 object centre (A): -1.707500 -37.34350 6.321000 number of atom coordinates read : 2741 total number of charged atoms : 2606 net assigned charge : 3.000016 assigned positive charge : 420.0883 centred at (gu) : 93.20618 89.71190 92.71607 assigned negative charge : -417.0894 centred at (gu) : 92.50346 90.91653 92.93504 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 203836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22912 grid for indexing accessible points = 1.400000 m= 106531 mr = 151839 m= 40820 mr = 88450 m= 10585 mr = 33443 m= 1790 mr = 8115 m= 150 mr = 1222 m= 6 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5019 time to turn everything in is 1.110000 number of dielectric boundary points 80573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20848 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) : 1.989679 object centre at (A) : -1.707500 -37.34350 6.321000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2328663 -0.3092524 midg,1,midg; midg,igrid,midg 0.9757475 -0.6714103 1,midg,midg; igrid,midg,midg -0.1692126 0.4244587 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.350000 now iterating at: 08:16:59 rms-change max change #iterations 11.14309 349.1825 at 10iterations 6.564579 151.3409 at 20iterations 3.870557 86.20078 at 30iterations 2.275001 42.27890 at 40iterations 1.333688 23.42971 at 50iterations 0.7808392 15.10811 at 60iterations 0.4570410 7.412043 at 70iterations 0.2666997 4.761360 at 80iterations 0.1558861 2.576252 at 90iterations 9.0931498E-02 1.477073 at 100iterations 5.3144589E-02 0.9258041 at 110iterations 3.1124528E-02 0.5573730 at 120iterations 1.8376209E-02 0.3406029 at 130iterations 1.0966662E-02 0.2193108 at 140iterations 6.6928407E-03 0.1418762 at 150iterations 4.2348192E-03 9.8571777E-02 at 160iterations 2.8343925E-03 6.8325043E-02 at 170iterations 2.0270094E-03 5.0117493E-02 at 180iterations finished qdiffx linear iterations at : 08:17:10 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 2.0270094E-03 5.0117493E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 08:17:10 12.780u 0.209s 0:13.31 97.5% 0+0k 0+0io 0pf+0w