Sat Oct 15 11:55:36 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 15 2011 at 11:55:36 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2226 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6491138 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): -13.87200 40.97200 ymin,ymax (A): -29.74900 24.09300 zmin,zma (A): -9.394000 34.80600 x,y,z range (A): 54.84400 53.84200 44.20000 scale (grids/A): 0.6491138 object centre (A): 13.55000 -2.828000 12.70600 number of atom coordinates read : 2226 total number of charged atoms : 2092 net assigned charge : 10.51402 assigned positive charge : 325.0737 centred at (gu) : 89.36420 91.23305 91.04675 assigned negative charge : -314.5603 centred at (gu) : 89.34202 91.22237 90.94037 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6595 nv = 96 ne = 84 npr = 43521 no. pairs analyzed = 43521 no. exposed pairs = 3134 no. arc points = 22176 no. surface atoms = 1034 nbur = 1192 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 3292 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2151 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5133502E-09 4.0201403E-08 midg,1,midg; midg,igrid,midg 1.4297784E-08 2.6938087E-08 1,midg,midg; igrid,midg,midg 1.9263318E-08 1.9565523E-08 gauss-seidel spectral radius is 0.9876822 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 11:55:37 rms-change max change #iterations 0.1365551 22.72283 at 10iterations 1.4160480E-02 2.134769 at 20iterations 1.4055355E-03 0.2028236 at 30iterations 1.4728222E-04 2.2186279E-02 at 40iterations 1.7194920E-05 2.6302338E-03 at 50iterations finished qdiffx linear iterations at : 11:55:40 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 1.7194920E-05 2.6302338E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 11:55:41 4.165u 0.288s 0:04.73 93.8% 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 15 2011 at 11:55:41 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2226 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.947341 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): -13.87200 40.97200 ymin,ymax (A): -29.74900 24.09300 zmin,zma (A): -9.394000 34.80600 x,y,z range (A): 54.84400 53.84200 44.20000 scale (grids/A): 1.947341 object centre (A): 13.55000 -2.828000 12.70600 number of atom coordinates read : 2226 total number of charged atoms : 2092 net assigned charge : 10.51402 assigned positive charge : 325.0737 centred at (gu) : 88.09246 93.69890 93.14034 assigned negative charge : -314.5603 centred at (gu) : 88.02624 93.66713 92.82134 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22176 grid for indexing accessible points = 1.400000 m= 26014 mr = 45898 m= 4746 mr = 18567 m= 354 mr = 2942 m= 1 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 33521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 16463 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) : 0.6491138 object centre at (A) : 13.55000 -2.828000 12.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9907964E-03 2.7975015E-02 midg,1,midg; midg,igrid,midg 4.4324964E-02 2.9969227E-02 1,midg,midg; igrid,midg,midg 5.5126283E-02 4.5564752E-02 gauss-seidel spectral radius is 0.9986712 estimated iterations to convergence 217 setup time was (sec) 0.9900000 now iterating at: 11:55:42 rms-change max change #iterations 3.965885 223.4246 at 10iterations 1.865709 64.16947 at 20iterations 0.8810884 31.19871 at 30iterations 0.4176402 13.48835 at 40iterations 0.1960981 6.567417 at 50iterations 9.2712350E-02 3.264328 at 60iterations 4.3657064E-02 1.438282 at 70iterations 2.0695588E-02 0.6621876 at 80iterations 9.7548543E-03 0.3322734 at 90iterations 4.5989659E-03 0.1434517 at 100iterations 2.1794040E-03 7.6873779E-02 at 110iterations 1.0330204E-03 3.5814285E-02 at 120iterations finished qdiffx linear iterations at : 11:55:51 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 1.0330204E-03 3.5814285E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 11:55:51 9.759u 0.310s 0:10.32 97.4% 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 Sat Oct 15 2011 at 11:55:51 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2226 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.921012 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): -13.87200 40.97200 ymin,ymax (A): -29.74900 24.09300 zmin,zma (A): -9.394000 34.80600 x,y,z range (A): 54.84400 53.84200 44.20000 scale (grids/A): 2.921012 object centre (A): 13.55000 -2.828000 12.70600 number of atom coordinates read : 2226 total number of charged atoms : 2092 net assigned charge : 10.51402 assigned positive charge : 325.0737 centred at (gu) : 87.13863 95.54823 94.71053 assigned negative charge : -314.5603 centred at (gu) : 87.03945 95.50080 94.23202 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22176 grid for indexing accessible points = 1.400000 m= 81398 mr = 111646 m= 32132 mr = 64952 m= 8596 mr = 25470 m= 1487 mr = 6307 m= 112 mr = 973 m= 0 mr = 39 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 75547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 16736 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) : 1.947341 object centre at (A) : 13.55000 -2.828000 12.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4022653E-02 0.2561305 midg,1,midg; midg,igrid,midg 0.6765512 0.3003155 1,midg,midg; igrid,midg,midg 0.5409251 0.4442359 gauss-seidel spectral radius is 0.9992762 estimated iterations to convergence 293 setup time was (sec) 2.010000 now iterating at: 11:55:54 rms-change max change #iterations 9.440184 343.7805 at 10iterations 5.584527 174.8327 at 20iterations 3.281050 74.74138 at 30iterations 1.925624 43.94023 at 40iterations 1.124480 22.62203 at 50iterations 0.6535965 14.30363 at 60iterations 0.3811722 8.007319 at 70iterations 0.2214034 4.728123 at 80iterations 0.1282184 2.663589 at 90iterations 7.4371144E-02 1.464227 at 100iterations 4.3089703E-02 0.8439837 at 110iterations 2.4985764E-02 0.4644861 at 120iterations 1.4488760E-02 0.2965980 at 130iterations 8.3777206E-03 0.1596756 at 140iterations 4.8524644E-03 9.3863487E-02 at 150iterations 2.8024693E-03 5.0806046E-02 at 160iterations 1.6251794E-03 3.1332970E-02 at 170iterations 9.4092445E-04 1.7268181E-02 at 180iterations finished qdiffx linear iterations at : 11:56:08 total time elapsed so far: 16.25000 # loops : 180 mean,max change (kT/e) : 9.4092445E-04 1.7268181E-02 energy calculations done at 16.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.44000 DelPhi exited at 11:56:08 16.441u 0.340s 0:17.06 98.3% 0+0k 0+0io 0pf+0w