Sat Oct 8 20:24:18 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 20:24:18 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7079364 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): -26.79700 22.13200 ymin,ymax (A): -11.00000 39.28700 zmin,zma (A): -40.24200 8.374001 x,y,z range (A): 48.92900 50.28700 48.61600 scale (grids/A): 0.7079364 object centre (A): -2.332500 14.14350 -15.93400 number of atom coordinates read : 2563 total number of charged atoms : 2419 net assigned charge : 3.934003 assigned positive charge : 386.6171 centred at (gu) : 88.57157 87.96343 89.47084 assigned negative charge : -382.6837 centred at (gu) : 88.45577 87.85982 89.55173 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8637 nv = 96 ne = 84 npr = 54225 no. pairs analyzed = 54225 no. exposed pairs = 2938 no. arc points = 21309 no. surface atoms = 987 nbur = 1576 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 561 mr = 5074 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 347 time to turn everything in is 0.3000000 number of dielectric boundary points 4026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1932 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3812410E-08 -1.2312162E-08 midg,1,midg; midg,igrid,midg -4.3494051E-08 6.6264185E-08 1,midg,midg; igrid,midg,midg -4.8194764E-08 7.9911871E-08 gauss-seidel spectral radius is 0.9896461 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 20:24:19 rms-change max change #iterations 0.2327983 33.73516 at 10iterations 2.8931050E-02 3.643753 at 20iterations 3.5864674E-03 0.4007416 at 30iterations 4.3924968E-04 6.4918518E-02 at 40iterations 5.5021312E-05 8.1672668E-03 at 50iterations finished qdiffx linear iterations at : 20:24:21 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 5.5021312E-05 8.1672668E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 20:24:22 3.227u 0.147s 0:03.65 92.0% 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 Sat Oct 8 2011 at 20:24:22 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 = 2563 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 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: 2.123809 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): -26.79700 22.13200 ymin,ymax (A): -11.00000 39.28700 zmin,zma (A): -40.24200 8.374001 x,y,z range (A): 48.92900 50.28700 48.61600 scale (grids/A): 2.123809 object centre (A): -2.332500 14.14350 -15.93400 number of atom coordinates read : 2563 total number of charged atoms : 2419 net assigned charge : 3.934003 assigned positive charge : 386.6171 centred at (gu) : 85.71405 83.88995 88.41202 assigned negative charge : -382.6837 centred at (gu) : 85.36722 83.57919 88.65500 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 36298 mr = 66068 m= 6819 mr = 28002 m= 665 mr = 4726 m= 7 mr = 357 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 9527 time to turn everything in is 0.6400000 number of dielectric boundary points 37079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19218 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) : 0.7079364 object centre at (A) : -2.332500 14.14350 -15.93400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8000593E-02 5.2164341E-03 midg,1,midg; midg,igrid,midg -3.9628137E-02 9.5136254E-04 1,midg,midg; igrid,midg,midg -1.7270762E-02 0.1173584 gauss-seidel spectral radius is 0.9988753 estimated iterations to convergence 236 setup time was (sec) 0.9200000 now iterating at: 20:24:23 rms-change max change #iterations 5.215731 200.7355 at 10iterations 2.598851 90.68593 at 20iterations 1.305149 37.08699 at 30iterations 0.6568241 19.59893 at 40iterations 0.3303244 8.668625 at 50iterations 0.1656114 4.409344 at 60iterations 8.3382495E-02 2.256176 at 70iterations 4.1897442E-02 1.213331 at 80iterations 2.0984519E-02 0.5722642 at 90iterations 1.0525607E-02 0.2939568 at 100iterations 5.3202100E-03 0.1493359 at 110iterations 2.6702408E-03 7.0811272E-02 at 120iterations finished qdiffx linear iterations at : 20:24:29 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 2.6702408E-03 7.0811272E-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) 7.230000 DelPhi exited at 20:24:30 7.228u 0.178s 0:07.71 95.8% 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 20:24:30 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2563 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.185714 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): -26.79700 22.13200 ymin,ymax (A): -11.00000 39.28700 zmin,zma (A): -40.24200 8.374001 x,y,z range (A): 48.92900 50.28700 48.61600 scale (grids/A): 3.185714 object centre (A): -2.332500 14.14350 -15.93400 number of atom coordinates read : 2563 total number of charged atoms : 2419 net assigned charge : 3.934003 assigned positive charge : 386.6171 centred at (gu) : 83.57111 80.83474 87.61783 assigned negative charge : -382.6837 centred at (gu) : 83.05072 80.36884 87.98240 start vw surface at 0.1400000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 213022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 114029 mr = 158425 m= 45936 mr = 96097 m= 12996 mr = 38334 m= 2633 mr = 10331 m= 315 mr = 2007 m= 7 mr = 213 m= 0 mr = 2 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 32087 time to turn everything in is 2.010000 number of dielectric boundary points 83529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 19352 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) : 2.123809 object centre at (A) : -2.332500 14.14350 -15.93400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2085579 0.1407936 midg,1,midg; midg,igrid,midg -0.1652354 -0.1233625 1,midg,midg; igrid,midg,midg -0.2369014 1.595115 gauss-seidel spectral radius is 0.9993151 estimated iterations to convergence 301 setup time was (sec) 2.300000 now iterating at: 20:24:32 rms-change max change #iterations 11.36330 396.3932 at 10iterations 6.668348 121.5526 at 20iterations 3.912665 78.11750 at 30iterations 2.297318 38.30058 at 40iterations 1.345265 21.04205 at 50iterations 0.7879443 13.09703 at 60iterations 0.4633570 7.259864 at 70iterations 0.2718802 4.217836 at 80iterations 0.1591005 2.611702 at 90iterations 9.3325660E-02 1.387363 at 100iterations 5.4749943E-02 0.8744826 at 110iterations 3.2102242E-02 0.5149250 at 120iterations 1.8808072E-02 0.3176112 at 130iterations 1.1031304E-02 0.1826687 at 140iterations 6.4663617E-03 0.1028500 at 150iterations 3.7899904E-03 5.9906006E-02 at 160iterations 2.2231294E-03 3.6174774E-02 at 170iterations 1.3047581E-03 2.1413803E-02 at 180iterations finished qdiffx linear iterations at : 20:24:42 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 1.3047581E-03 2.1413803E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 20:24:43 12.190u 0.202s 0:12.70 97.5% 0+0k 0+0io 0pf+0w