Sun Oct 9 00:31:32 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 00:31:32 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5395166 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): 87.70600 149.7650 ymin,ymax (A): 73.00000 138.9850 zmin,zma (A): -3.230000 45.92000 x,y,z range (A): 62.05900 65.98500 49.15000 scale (grids/A): 0.5395166 object centre (A): 118.7355 105.9925 21.34500 number of atom coordinates read : 3235 total number of charged atoms : 3093 net assigned charge : 10.74004 assigned positive charge : 478.9418 centred at (gu) : 91.25880 90.79939 90.76200 assigned negative charge : -468.2033 centred at (gu) : 91.13201 91.01112 90.68893 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6497 nv = 96 ne = 84 npr = 61882 no. pairs analyzed = 61882 no. exposed pairs = 4389 no. arc points = 31542 no. surface atoms = 1437 nbur = 1798 mkacc time = 0.1900000 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 = 1.568000 m= 262 mr = 3291 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3079 ## 390 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8275 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6409471E-11 1.1012093E-09 midg,1,midg; midg,igrid,midg 1.3448782E-09 -8.3263341E-10 1,midg,midg; igrid,midg,midg -1.3173122E-10 1.6425362E-09 gauss-seidel spectral radius is 0.9823276 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 00:31:33 rms-change max change #iterations 7.4599370E-02 12.11543 at 10iterations 4.7276928E-03 0.7540207 at 20iterations 3.3309046E-04 5.7216644E-02 at 30iterations 2.9185772E-05 5.0220490E-03 at 40iterations 3.9854040E-06 7.3432922E-04 at 50iterations finished qdiffx linear iterations at : 00:31:36 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 3.9854040E-06 7.3432922E-04 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 00:31:37 4.093u 0.164s 0:04.53 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 Sun Oct 9 2011 at 00:31:37 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.618550 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): 87.70600 149.7650 ymin,ymax (A): 73.00000 138.9850 zmin,zma (A): -3.230000 45.92000 x,y,z range (A): 62.05900 65.98500 49.15000 scale (grids/A): 1.618550 object centre (A): 118.7355 105.9925 21.34500 number of atom coordinates read : 3235 total number of charged atoms : 3093 net assigned charge : 10.74004 assigned positive charge : 478.9418 centred at (gu) : 93.77546 92.39758 92.28465 assigned negative charge : -468.2033 centred at (gu) : 93.39594 93.03307 92.06677 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 71437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31542 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22490 mr = 47379 m= 2375 mr = 15429 m= 71 mr = 1062 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.6600000 number of dielectric boundary points 32503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 408 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23615 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) : 0.5395166 object centre at (A) : 118.7355 105.9925 21.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6561531E-04 1.1677446E-02 midg,1,midg; midg,igrid,midg 2.2092469E-02 -1.6050618E-02 1,midg,midg; igrid,midg,midg -1.6513564E-02 2.5991151E-02 gauss-seidel spectral radius is 0.9981990 estimated iterations to convergence 187 setup time was (sec) 0.9900000 now iterating at: 00:31:38 rms-change max change #iterations 3.397230 170.1734 at 10iterations 1.410426 62.79588 at 20iterations 0.5901986 22.29454 at 30iterations 0.2450782 8.427708 at 40iterations 0.1026464 3.347049 at 50iterations 4.2957999E-02 1.447877 at 60iterations 1.7952949E-02 0.6185036 at 70iterations 7.5007603E-03 0.2456284 at 80iterations 3.1452975E-03 0.1207707 at 90iterations 1.3150679E-03 4.5120239E-02 at 100iterations 5.4871087E-04 1.9969940E-02 at 110iterations 2.3035020E-04 8.5258484E-03 at 120iterations finished qdiffx linear iterations at : 00:31:46 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 2.3035020E-04 8.5258484E-03 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.010000 DelPhi exited at 00:31:46 9.009u 0.179s 0:09.50 96.5% 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 00:31:46 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.427824 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): 87.70600 149.7650 ymin,ymax (A): 73.00000 138.9850 zmin,zma (A): -3.230000 45.92000 x,y,z range (A): 62.05900 65.98500 49.15000 scale (grids/A): 2.427824 object centre (A): 118.7355 105.9925 21.34500 number of atom coordinates read : 3235 total number of charged atoms : 3093 net assigned charge : 10.74004 assigned positive charge : 478.9418 centred at (gu) : 95.66290 93.59602 93.42673 assigned negative charge : -468.2033 centred at (gu) : 95.09399 94.54942 93.10029 start vw surface at 0.2100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 165695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31542 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77252 mr = 116333 m= 22531 mr = 60518 m= 3524 mr = 16765 m= 198 mr = 2161 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1197 time to turn everything in is 1.550000 number of dielectric boundary points 73374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 24697 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) : 1.618550 object centre at (A) : 118.7355 105.9925 21.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4131621E-03 0.1445424 midg,1,midg; midg,igrid,midg 0.4075143 -0.2102176 1,midg,midg; igrid,midg,midg -0.3889292 0.3969685 gauss-seidel spectral radius is 0.9991590 estimated iterations to convergence 272 setup time was (sec) 1.910000 now iterating at: 00:31:48 rms-change max change #iterations 8.974278 266.7208 at 10iterations 5.120575 147.6467 at 20iterations 2.907915 69.58365 at 30iterations 1.638258 43.99091 at 40iterations 0.9169704 21.36144 at 50iterations 0.5121529 10.40933 at 60iterations 0.2862507 6.193949 at 70iterations 0.1593973 3.006354 at 80iterations 8.8730283E-02 1.776524 at 90iterations 4.9245887E-02 0.9663277 at 100iterations 2.7263509E-02 0.5341835 at 110iterations 1.5121524E-02 0.3246260 at 120iterations 8.3767716E-03 0.1908393 at 130iterations 4.6439767E-03 9.3627691E-02 at 140iterations 2.5694785E-03 5.4482460E-02 at 150iterations 1.4233104E-03 2.9943466E-02 at 160iterations 7.8712276E-04 1.6681910E-02 at 170iterations 4.3463812E-04 9.0789795E-03 at 180iterations finished qdiffx linear iterations at : 00:32:01 total time elapsed so far: 14.32000 # loops : 180 mean,max change (kT/e) : 4.3463812E-04 9.0789795E-03 energy calculations done at 14.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 00:32:01 14.546u 0.195s 0:15.01 98.1% 0+0k 0+0io 0pf+0w