Mon Oct 10 14:02:03 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+sph.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 = amb.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 Mon Oct 10 2011 at 14:02:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 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: 0.5686265 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): 14.68000 68.47900 ymin,ymax (A): -20.38200 42.22500 zmin,zma (A): -28.52000 33.46900 x,y,z range (A): 53.79900 62.60700 61.98900 scale (grids/A): 0.5686265 object centre (A): 41.57950 10.92150 2.474501 number of atom coordinates read : 3503 total number of charged atoms : 3378 net assigned charge : 2.500002 assigned positive charge : 525.9147 centred at (gu) : 89.13834 89.09462 89.90009 assigned negative charge : -523.4168 centred at (gu) : 89.24037 89.09684 89.82143 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7413 nv = 96 ne = 84 npr = 66856 no. pairs analyzed = 66856 no. exposed pairs = 5390 no. arc points = 38798 no. surface atoms = 1752 nbur = 1751 mkacc time = 0.1100000 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 = 1.512000 m= 365 mr = 3111 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3775 ## 423 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0769881E-09 1.6824748E-09 midg,1,midg; midg,igrid,midg 4.7996379E-10 2.5254770E-10 1,midg,midg; igrid,midg,midg 2.6190665E-09 -1.1920451E-09 gauss-seidel spectral radius is 0.9841045 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 14:02:03 rms-change max change #iterations 9.6053496E-02 15.86793 at 10iterations 7.0420066E-03 1.055641 at 20iterations 5.9378898E-04 8.2347870E-02 at 30iterations 1.0704222E-04 1.5151978E-02 at 40iterations 3.3086304E-05 4.3835640E-03 at 50iterations finished qdiffx linear iterations at : 14:02:06 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 3.3086304E-05 4.3835640E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:02:07 3.451u 0.181s 0:04.37 83.0% 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 Mon Oct 10 2011 at 14:02:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 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: 1.705879 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): 14.68000 68.47900 ymin,ymax (A): -20.38200 42.22500 zmin,zma (A): -28.52000 33.46900 x,y,z range (A): 53.79900 62.60700 61.98900 scale (grids/A): 1.705879 object centre (A): 41.57950 10.92150 2.474501 number of atom coordinates read : 3503 total number of charged atoms : 3378 net assigned charge : 2.500002 assigned positive charge : 525.9147 centred at (gu) : 87.41422 87.28268 89.69924 assigned negative charge : -523.4168 centred at (gu) : 87.72109 87.29015 89.46394 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38798 grid for indexing accessible points = 1.400000 m= 24343 mr = 47620 m= 3279 mr = 14901 m= 169 mr = 1686 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.4100000 number of dielectric boundary points 43091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 26122 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) : 0.5686265 object centre at (A) : 41.57950 10.92150 2.474501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2688682E-02 1.7740496E-02 midg,1,midg; midg,igrid,midg -8.8127051E-03 1.3015521E-02 1,midg,midg; igrid,midg,midg 1.4539536E-02 -5.8681392E-03 gauss-seidel spectral radius is 0.9984300 estimated iterations to convergence 200 setup time was (sec) 0.6600000 now iterating at: 14:02:08 rms-change max change #iterations 4.014087 154.9859 at 10iterations 1.776417 60.41998 at 20iterations 0.7807301 26.19331 at 30iterations 0.3464176 12.23726 at 40iterations 0.1524021 4.951880 at 50iterations 6.7348704E-02 2.187164 at 60iterations 2.9900074E-02 1.104203 at 70iterations 1.3197429E-02 0.4111302 at 80iterations 5.8713504E-03 0.2013626 at 90iterations 2.6153671E-03 8.2851410E-02 at 100iterations 1.1807123E-03 4.0088654E-02 at 110iterations 5.4248364E-04 1.8514633E-02 at 120iterations finished qdiffx linear iterations at : 14:02:16 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 5.4248364E-04 1.8514633E-02 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 14:02:17 8.743u 0.259s 0:09.66 93.0% 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 Mon Oct 10 2011 at 14:02:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 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: 2.558819 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): 14.68000 68.47900 ymin,ymax (A): -20.38200 42.22500 zmin,zma (A): -28.52000 33.46900 x,y,z range (A): 53.79900 62.60700 61.98900 scale (grids/A): 2.558819 object centre (A): 41.57950 10.92150 2.474501 number of atom coordinates read : 3503 total number of charged atoms : 3378 net assigned charge : 2.500002 assigned positive charge : 525.9147 centred at (gu) : 86.12090 85.92367 89.54852 assigned negative charge : -523.4168 centred at (gu) : 86.58154 85.93532 89.19585 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38798 grid for indexing accessible points = 1.400000 m= 80058 mr = 118462 m= 25495 mr = 58234 m= 5410 mr = 17875 m= 646 mr = 3603 m= 21 mr = 359 m= 0 mr = 6 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 1.010000 number of dielectric boundary points 97334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 27009 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) : 1.705879 object centre at (A) : 41.57950 10.92150 2.474501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1476994 0.2312447 midg,1,midg; midg,igrid,midg -0.1594207 0.1547025 1,midg,midg; igrid,midg,midg 0.1744598 -0.1301109 gauss-seidel spectral radius is 0.9992464 estimated iterations to convergence 288 setup time was (sec) 1.310000 now iterating at: 14:02:19 rms-change max change #iterations 10.41378 294.3439 at 10iterations 6.199349 158.3630 at 20iterations 3.661603 93.26193 at 30iterations 2.148619 52.18161 at 40iterations 1.252593 29.34085 at 50iterations 0.7271906 16.08494 at 60iterations 0.4220840 9.643377 at 70iterations 0.2432235 5.644463 at 80iterations 0.1404986 2.855551 at 90iterations 8.0766790E-02 1.819908 at 100iterations 4.6528190E-02 0.9228973 at 110iterations 2.6756376E-02 0.5492477 at 120iterations 1.5326627E-02 0.2860250 at 130iterations 8.8051306E-03 0.1638870 at 140iterations 5.0487635E-03 9.7743988E-02 at 150iterations 2.8965152E-03 5.3896904E-02 at 160iterations 1.6628702E-03 2.9296875E-02 at 170iterations 9.5546624E-04 1.8402100E-02 at 180iterations finished qdiffx linear iterations at : 14:02:32 total time elapsed so far: 14.46000 # loops : 180 mean,max change (kT/e) : 9.5546624E-04 1.8402100E-02 energy calculations done at 14.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 14:02:32 14.592u 0.231s 0:15.18 97.6% 0+0k 0+0io 0pf+0w