Mon Oct 10 17:02:34 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 Mon Oct 10 2011 at 17:02:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 !!! WARNING: HIT 107 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5959556 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): -31.76900 27.96700 ymin,ymax (A): -8.233000 39.26800 zmin,zma (A): -3.850000 54.22300 x,y,z range (A): 59.73600 47.50100 58.07300 scale (grids/A): 0.5959556 object centre (A): -1.901000 15.51750 25.18650 number of atom coordinates read : 2908 total number of charged atoms : 2768 net assigned charge : 1.4020242E-02 assigned positive charge : 438.5620 centred at (gu) : 89.07673 89.58294 89.07018 assigned negative charge : -438.5492 centred at (gu) : 88.97819 89.44477 88.94890 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7068 nv = 96 ne = 84 npr = 57709 no. pairs analyzed = 57709 no. exposed pairs = 3849 no. arc points = 26930 no. surface atoms = 1294 nbur = 1614 mkacc time = 0.1200000 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 = 1.456000 m= 330 mr = 3724 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.3500000 number of dielectric boundary points 3654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2758 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8688 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3966986E-09 3.5946219E-09 midg,1,midg; midg,igrid,midg -5.4800298E-09 4.5852415E-09 1,midg,midg; igrid,midg,midg -4.3379336E-09 2.9506275E-09 gauss-seidel spectral radius is 0.9854622 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 17:02:35 rms-change max change #iterations 0.1128977 19.34563 at 10iterations 9.2430990E-03 1.430500 at 20iterations 7.7178312E-04 0.1201973 at 30iterations 6.4797794E-05 1.0290146E-02 at 40iterations 5.3814138E-06 7.7056885E-04 at 50iterations finished qdiffx linear iterations at : 17:02:37 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 5.3814138E-06 7.7056885E-04 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 17:02:38 3.259u 0.159s 0:04.55 74.7% 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 Mon Oct 10 2011 at 17:02:38 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.787867 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): -31.76900 27.96700 ymin,ymax (A): -8.233000 39.26800 zmin,zma (A): -3.850000 54.22300 x,y,z range (A): 59.73600 47.50100 58.07300 scale (grids/A): 1.787867 object centre (A): -1.901000 15.51750 25.18650 number of atom coordinates read : 2908 total number of charged atoms : 2768 net assigned charge : 1.4020242E-02 assigned positive charge : 438.5620 centred at (gu) : 87.22929 88.74790 87.20950 assigned negative charge : -438.5492 centred at (gu) : 86.93408 88.33390 86.84627 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26930 grid for indexing accessible points = 1.400000 m= 26504 mr = 51676 m= 3444 mr = 19089 m= 112 mr = 1885 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1314 time to turn everything in is 0.5400000 number of dielectric boundary points 33756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21629 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) : 0.5959556 object centre at (A) : -1.901000 15.51750 25.18650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7462859E-03 1.9307455E-02 midg,1,midg; midg,igrid,midg -2.1224681E-02 1.0185641E-02 1,midg,midg; igrid,midg,midg -3.2437015E-02 2.1430243E-02 gauss-seidel spectral radius is 0.9984916 estimated iterations to convergence 204 setup time was (sec) 0.8100000 now iterating at: 17:02:39 rms-change max change #iterations 4.010641 167.8645 at 10iterations 1.794752 64.43138 at 20iterations 0.8073796 27.01901 at 30iterations 0.3632353 12.56817 at 40iterations 0.1631895 5.745526 at 50iterations 7.3555000E-02 2.430818 at 60iterations 3.3078253E-02 1.090282 at 70iterations 1.4850140E-02 0.5048132 at 80iterations 6.6816150E-03 0.2442379 at 90iterations 3.0178095E-03 0.1118832 at 100iterations 1.3545459E-03 4.6004295E-02 at 110iterations 6.1264139E-04 2.2211075E-02 at 120iterations finished qdiffx linear iterations at : 17:02:46 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 6.1264139E-04 2.2211075E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 17:02:47 8.091u 0.170s 0:08.70 94.9% 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 Mon Oct 10 2011 at 17:02:47 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.681800 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): -31.76900 27.96700 ymin,ymax (A): -8.233000 39.26800 zmin,zma (A): -3.850000 54.22300 x,y,z range (A): 59.73600 47.50100 58.07300 scale (grids/A): 2.681800 object centre (A): -1.901000 15.51750 25.18650 number of atom coordinates read : 2908 total number of charged atoms : 2768 net assigned charge : 1.4020242E-02 assigned positive charge : 438.5620 centred at (gu) : 85.84382 88.12174 85.81419 assigned negative charge : -438.5492 centred at (gu) : 85.40118 87.50079 85.26935 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 176596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26930 grid for indexing accessible points = 1.400000 m= 87296 mr = 125803 m= 29261 mr = 70280 m= 5832 mr = 22823 m= 536 mr = 4146 m= 23 mr = 301 m= 0 mr = 2 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 4537 time to turn everything in is 1.270000 number of dielectric boundary points 76189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 22143 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) : 1.787867 object centre at (A) : -1.901000 15.51750 25.18650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2818940 0.2851316 midg,1,midg; midg,igrid,midg -0.2227770 0.1288918 1,midg,midg; igrid,midg,midg -0.4971549 0.2889675 gauss-seidel spectral radius is 0.9992324 estimated iterations to convergence 285 setup time was (sec) 1.560000 now iterating at: 17:02:49 rms-change max change #iterations 9.856766 287.8289 at 10iterations 5.724562 157.5452 at 20iterations 3.292325 70.18269 at 30iterations 1.894127 40.97999 at 40iterations 1.082369 20.33514 at 50iterations 0.6191881 13.10892 at 60iterations 0.3533051 6.632935 at 70iterations 0.2015403 3.805366 at 80iterations 0.1146536 2.082324 at 90iterations 6.5343216E-02 1.318655 at 100iterations 3.7121657E-02 0.7238957 at 110iterations 2.1093726E-02 0.3793135 at 120iterations 1.1996008E-02 0.2017250 at 130iterations 6.8236962E-03 0.1356211 at 140iterations 3.8790179E-03 7.4402332E-02 at 150iterations 2.2072482E-03 3.9816380E-02 at 160iterations 1.2486493E-03 2.3250580E-02 at 170iterations 7.1016414E-04 1.3870239E-02 at 180iterations finished qdiffx linear iterations at : 17:02:59 total time elapsed so far: 11.39000 # loops : 180 mean,max change (kT/e) : 7.1016414E-04 1.3870239E-02 energy calculations done at 11.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 17:03:00 11.565u 0.192s 0:12.49 94.0% 0+0k 0+0io 0pf+0w