Sun Oct 9 01:56:40 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 01:56:40 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6339596 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): 14.19300 68.12800 ymin,ymax (A): -30.55600 25.59900 zmin,zma (A): 2.565000 45.84700 x,y,z range (A): 53.93500 56.15500 43.28200 scale (grids/A): 0.6339596 object centre (A): 41.16050 -2.478499 24.20600 number of atom coordinates read : 2416 total number of charged atoms : 2281 net assigned charge : 11.51402 assigned positive charge : 357.2001 centred at (gu) : 89.85974 90.52548 89.48864 assigned negative charge : -345.6870 centred at (gu) : 89.87299 90.54642 89.60197 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6859 nv = 96 ne = 84 npr = 47269 no. pairs analyzed = 47269 no. exposed pairs = 3197 no. arc points = 22789 no. surface atoms = 1081 nbur = 1335 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 3642 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6635872E-08 3.5855421E-09 midg,1,midg; midg,igrid,midg 1.4213893E-08 1.3579459E-08 1,midg,midg; igrid,midg,midg 1.5642573E-08 1.2490284E-08 gauss-seidel spectral radius is 0.9871056 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 01:56:40 rms-change max change #iterations 0.1362457 24.66356 at 10iterations 1.3080633E-02 1.978327 at 20iterations 1.3565815E-03 0.1829758 at 30iterations 2.2241737E-04 4.4738770E-02 at 40iterations 7.0601636E-05 1.5509605E-02 at 50iterations finished qdiffx linear iterations at : 01:56:43 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 7.0601636E-05 1.5509605E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 01:56:44 3.331u 0.170s 0:03.78 92.5% 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 01:56:44 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.901879 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): 14.19300 68.12800 ymin,ymax (A): -30.55600 25.59900 zmin,zma (A): 2.565000 45.84700 x,y,z range (A): 53.93500 56.15500 43.28200 scale (grids/A): 1.901879 object centre (A): 41.16050 -2.478499 24.20600 number of atom coordinates read : 2416 total number of charged atoms : 2281 net assigned charge : 11.51402 assigned positive charge : 357.2001 centred at (gu) : 89.57874 91.57600 88.46557 assigned negative charge : -345.6870 centred at (gu) : 89.61889 91.63921 88.80596 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73187 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 27020 mr = 49653 m= 4593 mr = 19601 m= 299 mr = 2851 m= 8 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 32907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17950 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) : 0.6339596 object centre at (A) : 41.16050 -2.478499 24.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0189980E-02 -7.8117091E-04 midg,1,midg; midg,igrid,midg 5.6332275E-02 2.4839832E-02 1,midg,midg; igrid,midg,midg 5.9521947E-02 4.6506759E-02 gauss-seidel spectral radius is 0.9986265 estimated iterations to convergence 214 setup time was (sec) 0.5600000 now iterating at: 01:56:44 rms-change max change #iterations 4.030578 198.5863 at 10iterations 1.870910 68.04522 at 20iterations 0.8750060 30.45007 at 30iterations 0.4055823 13.95966 at 40iterations 0.1895289 5.704033 at 50iterations 8.8523030E-02 3.165148 at 60iterations 4.1405000E-02 1.244324 at 70iterations 1.9304093E-02 0.6707993 at 80iterations 9.0405978E-03 0.3094578 at 90iterations 4.2359442E-03 0.1441650 at 100iterations 2.0008541E-03 6.7835808E-02 at 110iterations 9.5911039E-04 3.6106110E-02 at 120iterations finished qdiffx linear iterations at : 01:56:52 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 9.5911039E-04 3.6106110E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 01:56:52 7.750u 0.210s 0:08.23 96.7% 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 Sun Oct 9 2011 at 01:56:52 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.852818 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): 14.19300 68.12800 ymin,ymax (A): -30.55600 25.59900 zmin,zma (A): 2.565000 45.84700 x,y,z range (A): 53.93500 56.15500 43.28200 scale (grids/A): 2.852818 object centre (A): 41.16050 -2.478499 24.20600 number of atom coordinates read : 2416 total number of charged atoms : 2281 net assigned charge : 11.51402 assigned positive charge : 357.2001 centred at (gu) : 89.36790 92.36389 87.69813 assigned negative charge : -345.6870 centred at (gu) : 89.42843 92.45886 88.20889 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 169308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 85996 mr = 120910 m= 32007 mr = 69653 m= 8311 mr = 25441 m= 1284 mr = 6134 m= 84 mr = 798 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 74041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18246 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) : 1.901879 object centre at (A) : 41.16050 -2.478499 24.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3015659 -2.3791434E-02 midg,1,midg; midg,igrid,midg 0.7419949 0.3007386 1,midg,midg; igrid,midg,midg 0.6507992 0.4817314 gauss-seidel spectral radius is 0.9992613 estimated iterations to convergence 290 setup time was (sec) 1.160000 now iterating at: 01:56:53 rms-change max change #iterations 9.512879 466.0192 at 10iterations 5.559967 128.4606 at 20iterations 3.230110 75.34509 at 30iterations 1.877619 41.06781 at 40iterations 1.088265 26.23330 at 50iterations 0.6297272 11.87278 at 60iterations 0.3628584 7.694338 at 70iterations 0.2099265 4.422710 at 80iterations 0.1207740 2.274170 at 90iterations 6.9583043E-02 1.431664 at 100iterations 4.0116571E-02 0.7582245 at 110iterations 2.3068128E-02 0.4344616 at 120iterations 1.3298160E-02 0.2656145 at 130iterations 7.6298309E-03 0.1610794 at 140iterations 4.4002528E-03 7.6694489E-02 at 150iterations 2.5290493E-03 4.4231415E-02 at 160iterations 1.4606831E-03 2.7294159E-02 at 170iterations 8.4449962E-04 1.5818596E-02 at 180iterations finished qdiffx linear iterations at : 01:57:05 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 8.4449962E-04 1.5818596E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 01:57:05 12.802u 0.217s 0:13.29 97.8% 0+0k 0+0io 0pf+0w