Tue Oct 11 00:20:55 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 Tue Oct 11 2011 at 00:20:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5195867 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): -21.04100 40.58000 ymin,ymax (A): 10.20000 75.58000 zmin,zma (A): -15.28200 53.23400 x,y,z range (A): 61.62100 65.38000 68.51600 scale (grids/A): 0.5195867 object centre (A): 9.769501 42.89000 18.97600 number of atom coordinates read : 3958 total number of charged atoms : 3807 net assigned charge : 10.00004 assigned positive charge : 608.0255 centred at (gu) : 91.14944 89.94267 91.67709 assigned negative charge : -598.0278 centred at (gu) : 91.19695 90.09581 91.63633 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6757 nv = 96 ne = 84 npr = 77668 no. pairs analyzed = 77668 no. exposed pairs = 5117 no. arc points = 35727 no. surface atoms = 1717 nbur = 2241 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 226 mr = 3318 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3800000 number of dielectric boundary points 3662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3636 ## 588 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4240550E-11 5.2004584E-10 midg,1,midg; midg,igrid,midg 6.9261219E-10 -2.7922031E-10 1,midg,midg; igrid,midg,midg 2.6710323E-10 7.5317648E-11 gauss-seidel spectral radius is 0.9809985 estimated iterations to convergence 60 setup time was (sec) 0.6100000 now iterating at: 00:20:56 rms-change max change #iterations 6.7743778E-02 10.38036 at 10iterations 5.0905016E-03 1.009842 at 20iterations 7.9267321E-04 0.2080917 at 30iterations 1.7607833E-04 4.8751831E-02 at 40iterations 4.0855852E-05 1.1432648E-02 at 50iterations finished qdiffx linear iterations at : 00:20:58 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 4.0855852E-05 1.1432648E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 00:20:59 3.412u 0.186s 0:03.97 90.4% 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 00:20:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 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: 1.558760 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): -21.04100 40.58000 ymin,ymax (A): 10.20000 75.58000 zmin,zma (A): -15.28200 53.23400 x,y,z range (A): 61.62100 65.38000 68.51600 scale (grids/A): 1.558760 object centre (A): 9.769501 42.89000 18.97600 number of atom coordinates read : 3958 total number of charged atoms : 3807 net assigned charge : 10.00004 assigned positive charge : 608.0255 centred at (gu) : 93.44688 89.82743 95.03014 assigned negative charge : -598.0278 centred at (gu) : 93.59042 90.28697 94.90843 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21249 mr = 50528 m= 1669 mr = 13812 m= 29 mr = 646 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.5300000 number of dielectric boundary points 34066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 469 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 28764 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) : 0.5195867 object centre at (A) : 9.769501 42.89000 18.97600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0440616E-02 7.4649840E-03 midg,1,midg; midg,igrid,midg 2.1951841E-02 1.2713733E-02 1,midg,midg; igrid,midg,midg 3.2287494E-03 1.6223395E-02 gauss-seidel spectral radius is 0.9980910 estimated iterations to convergence 182 setup time was (sec) 0.8300000 now iterating at: 00:21:00 rms-change max change #iterations 3.545264 147.5061 at 10iterations 1.441095 48.94914 at 20iterations 0.5852613 21.73181 at 30iterations 0.2392711 8.997422 at 40iterations 9.7870789E-02 3.390541 at 50iterations 4.0049884E-02 1.350652 at 60iterations 1.6451152E-02 0.5843582 at 70iterations 6.8315659E-03 0.2447376 at 80iterations 2.9168569E-03 0.1037884 at 90iterations 1.3031022E-03 5.4636002E-02 at 100iterations 6.0952466E-04 2.9089689E-02 at 110iterations 3.0892191E-04 1.6519547E-02 at 120iterations finished qdiffx linear iterations at : 00:21:06 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 3.0892191E-04 1.6519547E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 00:21:07 7.432u 0.209s 0:08.20 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 Tue Oct 11 2011 at 00:21:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3958 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: 2.338140 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): -21.04100 40.58000 ymin,ymax (A): 10.20000 75.58000 zmin,zma (A): -15.28200 53.23400 x,y,z range (A): 61.62100 65.38000 68.51600 scale (grids/A): 2.338140 object centre (A): 9.769501 42.89000 18.97600 number of atom coordinates read : 3958 total number of charged atoms : 3807 net assigned charge : 10.00004 assigned positive charge : 608.0255 centred at (gu) : 95.17027 89.74078 97.54491 assigned negative charge : -598.0278 centred at (gu) : 95.38561 90.43033 97.36253 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 177223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35727 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 76122 mr = 124427 m= 18776 mr = 58469 m= 2374 mr = 13490 m= 84 mr = 1303 m= 0 mr = 24 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 1.270000 number of dielectric boundary points 76866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 30394 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) : 1.558760 object centre at (A) : 9.769501 42.89000 18.97600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2581165 0.1233609 midg,1,midg; midg,igrid,midg 0.3173773 0.2182635 1,midg,midg; igrid,midg,midg 8.6142875E-02 0.2974072 gauss-seidel spectral radius is 0.9991271 estimated iterations to convergence 267 setup time was (sec) 1.580000 now iterating at: 00:21:09 rms-change max change #iterations 9.511194 362.8700 at 10iterations 5.350138 138.5841 at 20iterations 2.988895 73.48600 at 30iterations 1.662458 36.24699 at 40iterations 0.9209463 19.14456 at 50iterations 0.5097622 11.35143 at 60iterations 0.2809549 6.278660 at 70iterations 0.1545810 3.198448 at 80iterations 8.4995039E-02 1.729030 at 90iterations 4.6761122E-02 0.8924599 at 100iterations 2.5738051E-02 0.5195160 at 110iterations 1.4157588E-02 0.2807083 at 120iterations 7.7913548E-03 0.1599884 at 130iterations 4.3035364E-03 9.0133667E-02 at 140iterations 2.3944562E-03 5.0682068E-02 at 150iterations 1.3431407E-03 3.1078339E-02 at 160iterations 7.6453993E-04 1.9023895E-02 at 170iterations 4.4596478E-04 1.1146545E-02 at 180iterations finished qdiffx linear iterations at : 00:21:19 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 4.4596478E-04 1.1146545E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 00:21:20 12.039u 0.217s 0:12.57 97.3% 0+0k 0+0io 0pf+0w