Sat Oct 8 18:11:13 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 Sat Oct 8 2011 at 18:11:13 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 = 4699 !!! WARNING: GLM 76 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5096855 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): -1.136000 61.15200 ymin,ymax (A): -30.04800 30.78600 zmin,zma (A): -22.85000 46.99700 x,y,z range (A): 62.28800 60.83400 69.84700 scale (grids/A): 0.5096855 object centre (A): 30.00800 0.3689995 12.07350 number of atom coordinates read : 4699 total number of charged atoms : 4540 net assigned charge : -11.09397 assigned positive charge : 719.8068 centred at (gu) : 90.81660 91.18332 90.60594 assigned negative charge : -730.9059 centred at (gu) : 90.83312 91.14841 90.61120 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7882 nv = 96 ne = 84 npr = 92651 no. pairs analyzed = 92651 no. exposed pairs = 6182 no. arc points = 43528 no. surface atoms = 2058 nbur = 2641 mkacc time = 0.3100000 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= 281 mr = 3883 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4301 ## 647 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 10541 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1839794E-10 -1.9286175E-10 midg,1,midg; midg,igrid,midg -1.7728120E-10 -8.3855763E-11 1,midg,midg; igrid,midg,midg -8.9253507E-11 -2.3953886E-10 gauss-seidel spectral radius is 0.9803210 estimated iterations to convergence 59 setup time was (sec) 0.9600000 now iterating at: 18:11:14 rms-change max change #iterations 6.5116674E-02 9.187990 at 10iterations 3.6968919E-03 0.6132288 at 20iterations 2.9551773E-04 4.3800354E-02 at 30iterations 5.0304679E-05 9.1662407E-03 at 40iterations 1.1362789E-05 2.0556450E-03 at 50iterations finished qdiffx linear iterations at : 18:11:18 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 1.1362789E-05 2.0556450E-03 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 18:11:18 4.786u 0.402s 0:05.47 94.6% 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 Sat Oct 8 2011 at 18:11:18 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 = 4699 !!! WARNING: GLM 76 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.529056 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): -1.136000 61.15200 ymin,ymax (A): -30.04800 30.78600 zmin,zma (A): -22.85000 46.99700 x,y,z range (A): 62.28800 60.83400 69.84700 scale (grids/A): 1.529056 object centre (A): 30.00800 0.3689995 12.07350 number of atom coordinates read : 4699 total number of charged atoms : 4540 net assigned charge : -11.09397 assigned positive charge : 719.8068 centred at (gu) : 92.44830 93.54829 91.81648 assigned negative charge : -730.9059 centred at (gu) : 92.49914 93.44495 91.83349 start vw surface at 0.2300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 88646 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43528 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25138 mr = 58978 m= 2149 mr = 16293 m= 48 mr = 856 m= 0 mr = 1 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.9100000 number of dielectric boundary points 39853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 584 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 34076 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) : 0.5096855 object centre at (A) : 30.00800 0.3689995 12.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1500994E-03 -2.2986839E-02 midg,1,midg; midg,igrid,midg -1.4847163E-02 -8.4912051E-03 1,midg,midg; igrid,midg,midg 3.5385806E-03 -2.2374461E-03 gauss-seidel spectral radius is 0.9981044 estimated iterations to convergence 183 setup time was (sec) 1.240000 now iterating at: 18:11:20 rms-change max change #iterations 3.802083 162.8192 at 10iterations 1.550172 52.22558 at 20iterations 0.6337696 19.87272 at 30iterations 0.2590798 8.568555 at 40iterations 0.1059643 3.576954 at 50iterations 4.3268170E-02 1.388224 at 60iterations 1.7767016E-02 0.5460052 at 70iterations 7.2756256E-03 0.2534580 at 80iterations 2.9987795E-03 9.8314285E-02 at 90iterations 1.2322484E-03 4.0168762E-02 at 100iterations 5.1522639E-04 1.6496360E-02 at 110iterations 2.1718431E-04 7.4691772E-03 at 120iterations finished qdiffx linear iterations at : 18:11:29 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 2.1718431E-04 7.4691772E-03 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 18:11:29 10.597u 0.454s 0:11.40 96.8% 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 Sat Oct 8 2011 at 18:11:30 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 = 4699 !!! WARNING: GLM 76 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.293585 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): -1.136000 61.15200 ymin,ymax (A): -30.04800 30.78600 zmin,zma (A): -22.85000 46.99700 x,y,z range (A): 62.28800 60.83400 69.84700 scale (grids/A): 2.293585 object centre (A): 30.00800 0.3689995 12.07350 number of atom coordinates read : 4699 total number of charged atoms : 4540 net assigned charge : -11.09397 assigned positive charge : 719.8068 centred at (gu) : 93.67210 95.32211 92.72402 assigned negative charge : -730.9059 centred at (gu) : 93.74876 95.16727 92.75019 start vw surface at 0.2300000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 206319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43528 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90000 mr = 145067 m= 22311 mr = 69245 m= 3051 mr = 15765 m= 174 mr = 1705 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 525 time to turn everything in is 2.190000 number of dielectric boundary points 90027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 36218 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) : 1.529056 object centre at (A) : 30.00800 0.3689995 12.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2068118 -0.2871047 midg,1,midg; midg,igrid,midg -0.3636525 -0.1439345 1,midg,midg; igrid,midg,midg 4.3455154E-02 -8.7836131E-02 gauss-seidel spectral radius is 0.9991586 estimated iterations to convergence 272 setup time was (sec) 2.560000 now iterating at: 18:11:33 rms-change max change #iterations 10.40306 311.9702 at 10iterations 5.998153 160.3436 at 20iterations 3.423607 74.02734 at 30iterations 1.942336 38.27503 at 40iterations 1.095066 23.74223 at 50iterations 0.6152350 12.13976 at 60iterations 0.3447689 6.368711 at 70iterations 0.1925761 4.034576 at 80iterations 0.1075338 2.032581 at 90iterations 5.9920575E-02 1.137074 at 100iterations 3.3343140E-02 0.6713333 at 110iterations 1.8589705E-02 0.3951292 at 120iterations 1.0302671E-02 0.2068901 at 130iterations 5.7289591E-03 0.1081457 at 140iterations 3.1828070E-03 6.4876080E-02 at 150iterations 1.7663671E-03 3.2730043E-02 at 160iterations 9.8243589E-04 1.9317627E-02 at 170iterations 5.4633536E-04 9.5672607E-03 at 180iterations finished qdiffx linear iterations at : 18:11:48 total time elapsed so far: 18.40000 # loops : 180 mean,max change (kT/e) : 5.4633536E-04 9.5672607E-03 energy calculations done at 18.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.61000 DelPhi exited at 18:11:49 18.613u 0.476s 0:19.38 98.4% 0+0k 0+0io 0pf+0w