Sun Oct 9 16:58:28 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 Sun Oct 9 2011 at 16:58:28 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 = 5043 !!! WARNING: GLM 282 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5156804 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): 3.122000 66.26900 ymin,ymax (A): -0.9190000 54.15900 zmin,zma (A): -36.17700 32.85800 x,y,z range (A): 63.14700 55.07800 69.03500 scale (grids/A): 0.5156804 object centre (A): 34.69550 26.62000 -1.659500 number of atom coordinates read : 5043 total number of charged atoms : 4883 net assigned charge : 10.90605 assigned positive charge : 763.6153 centred at (gu) : 89.85603 90.53045 90.29426 assigned negative charge : -752.7150 centred at (gu) : 89.92694 90.62787 90.14757 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8284 nv = 96 ne = 84 npr = 103749 no. pairs analyzed = 103749 no. exposed pairs = 5908 no. arc points = 40425 no. surface atoms = 2004 nbur = 3039 mkacc time = 0.2200000 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 = 1.680000 m= 281 mr = 4480 m= 0 mr = 4 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4400000 number of dielectric boundary points 4081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4130 ## 632 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 11357 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8891486E-10 7.3711925E-10 midg,1,midg; midg,igrid,midg 4.5349624E-10 -1.6312050E-10 1,midg,midg; igrid,midg,midg 4.4916440E-10 -4.6342121E-11 gauss-seidel spectral radius is 0.9807771 estimated iterations to convergence 60 setup time was (sec) 0.6500000 now iterating at: 16:58:29 rms-change max change #iterations 7.6859623E-02 13.76789 at 10iterations 6.0461313E-03 0.7971725 at 20iterations 1.4921975E-03 0.2513199 at 30iterations 6.0451293E-04 0.1041679 at 40iterations 2.5250384E-04 4.4107437E-02 at 50iterations finished qdiffx linear iterations at : 16:58:31 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 2.5250384E-04 4.4107437E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 16:58:32 3.274u 0.162s 0:03.73 91.9% 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 Sun Oct 9 2011 at 16:58:32 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 = 5043 !!! WARNING: GLM 282 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.547041 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): 3.122000 66.26900 ymin,ymax (A): -0.9190000 54.15900 zmin,zma (A): -36.17700 32.85800 x,y,z range (A): 63.14700 55.07800 69.03500 scale (grids/A): 1.547041 object centre (A): 34.69550 26.62000 -1.659500 number of atom coordinates read : 5043 total number of charged atoms : 4883 net assigned charge : 10.90605 assigned positive charge : 763.6153 centred at (gu) : 89.56613 91.58994 90.88113 assigned negative charge : -752.7150 centred at (gu) : 89.78046 91.88335 90.44259 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 94987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26796 mr = 67147 m= 2286 mr = 18072 m= 45 mr = 978 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 336 time to turn everything in is 0.6200000 number of dielectric boundary points 37917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 615 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 36802 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) : 0.5156804 object centre at (A) : 34.69550 26.62000 -1.659500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8681111E-02 3.8661361E-02 midg,1,midg; midg,igrid,midg 1.5871486E-02 -2.4194845E-03 1,midg,midg; igrid,midg,midg 2.2368742E-02 8.4975278E-03 gauss-seidel spectral radius is 0.9981660 estimated iterations to convergence 186 setup time was (sec) 0.9000000 now iterating at: 16:58:33 rms-change max change #iterations 3.979999 156.1009 at 10iterations 1.647096 51.02179 at 20iterations 0.6877306 20.72178 at 30iterations 0.2860833 8.349849 at 40iterations 0.1191198 3.805678 at 50iterations 4.9900066E-02 1.512735 at 60iterations 2.1026375E-02 0.7053862 at 70iterations 9.1432361E-03 0.3268185 at 80iterations 4.2485478E-03 0.1496201 at 90iterations 2.2424047E-03 7.5965881E-02 at 100iterations 1.3645354E-03 4.9350739E-02 at 110iterations 9.2099514E-04 3.2978058E-02 at 120iterations finished qdiffx linear iterations at : 16:58:39 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 9.2099514E-04 3.2978058E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 16:58:40 7.255u 0.178s 0:07.69 96.4% 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 Sun Oct 9 2011 at 16:58:40 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 = 5043 !!! WARNING: GLM 282 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.320562 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): 3.122000 66.26900 ymin,ymax (A): -0.9190000 54.15900 zmin,zma (A): -36.17700 32.85800 x,y,z range (A): 63.14700 55.07800 69.03500 scale (grids/A): 2.320562 object centre (A): 34.69550 26.62000 -1.659500 number of atom coordinates read : 5043 total number of charged atoms : 4883 net assigned charge : 10.90605 assigned positive charge : 763.6153 centred at (gu) : 89.34883 92.38436 91.32126 assigned negative charge : -752.7150 centred at (gu) : 89.67071 92.82473 90.66389 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 222299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 97275 mr = 164901 m= 23815 mr = 76767 m= 3189 mr = 17260 m= 149 mr = 2012 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1141 time to turn everything in is 1.530000 number of dielectric boundary points 85750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 38975 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) : 1.547041 object centre at (A) : 34.69550 26.62000 -1.659500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4387950 0.6134183 midg,1,midg; midg,igrid,midg 0.2251677 -4.9604390E-02 1,midg,midg; igrid,midg,midg 0.3594269 0.2167191 gauss-seidel spectral radius is 0.9991790 estimated iterations to convergence 276 setup time was (sec) 1.850000 now iterating at: 16:58:42 rms-change max change #iterations 10.77110 286.0012 at 10iterations 6.233274 153.7760 at 20iterations 3.578037 76.21025 at 30iterations 2.040436 50.23304 at 40iterations 1.159331 23.85054 at 50iterations 0.6540980 12.66040 at 60iterations 0.3697772 7.203028 at 70iterations 0.2077783 4.234310 at 80iterations 0.1170230 2.306560 at 90iterations 6.5777570E-02 1.165878 at 100iterations 3.6917765E-02 0.6967547 at 110iterations 2.0729709E-02 0.3806744 at 120iterations 1.1618549E-02 0.2115991 at 130iterations 6.5356395E-03 0.1215787 at 140iterations 3.6861324E-03 6.5437317E-02 at 150iterations 2.0925272E-03 4.2445183E-02 at 160iterations 1.2017252E-03 2.2835732E-02 at 170iterations 7.1222894E-04 1.4949799E-02 at 180iterations finished qdiffx linear iterations at : 16:58:52 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 7.1222894E-04 1.4949799E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 16:58:53 12.650u 0.226s 0:13.14 97.9% 0+0k 0+0io 0pf+0w