Sun Oct 9 14:35:25 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 Sun Oct 9 2011 at 14:35:25 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 = 2693 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: 0.5686175 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): -0.1650001 52.51700 ymin,ymax (A): -9.233000 39.80900 zmin,zma (A): -15.63700 46.97100 x,y,z range (A): 52.68200 49.04200 62.60800 scale (grids/A): 0.5686175 object centre (A): 26.17600 15.28800 15.66700 number of atom coordinates read : 2693 total number of charged atoms : 2553 net assigned charge : 7.000018 assigned positive charge : 407.5164 centred at (gu) : 89.60734 90.34328 88.51638 assigned negative charge : -400.5174 centred at (gu) : 89.56596 90.24600 88.55025 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5696 nv = 96 ne = 84 npr = 53320 no. pairs analyzed = 53320 no. exposed pairs = 3502 no. arc points = 24919 no. surface atoms = 1178 nbur = 1515 mkacc time = 9.0000004E-02 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= 246 mr = 2835 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2527 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0797979E-09 3.9835990E-10 midg,1,midg; midg,igrid,midg -2.8725008E-10 2.5007694E-09 1,midg,midg; igrid,midg,midg 4.8927057E-10 1.4266071E-09 gauss-seidel spectral radius is 0.9840215 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 14:35:25 rms-change max change #iterations 8.4013395E-02 14.17064 at 10iterations 6.2620067E-03 1.187744 at 20iterations 4.8166330E-04 8.0085754E-02 at 30iterations 4.1305306E-05 7.5149536E-03 at 40iterations 4.9276191E-06 9.6511841E-04 at 50iterations finished qdiffx linear iterations at : 14:35:28 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.9276191E-06 9.6511841E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:35:29 3.385u 0.177s 0:03.90 91.0% 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 Sun Oct 9 2011 at 14:35:29 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 = 2693 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: 1.705852 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): -0.1650001 52.51700 ymin,ymax (A): -9.233000 39.80900 zmin,zma (A): -15.63700 46.97100 x,y,z range (A): 52.68200 49.04200 62.60800 scale (grids/A): 1.705852 object centre (A): 26.17600 15.28800 15.66700 number of atom coordinates read : 2693 total number of charged atoms : 2553 net assigned charge : 7.000018 assigned positive charge : 407.5164 centred at (gu) : 88.82156 91.02926 85.54843 assigned negative charge : -400.5174 centred at (gu) : 88.69743 90.73778 85.65060 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24919 grid for indexing accessible points = 1.400000 m= 19753 mr = 41461 m= 2155 mr = 13329 m= 53 mr = 1003 m= 0 mr = 2 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 28636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19756 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) : 0.5686175 object centre at (A) : 26.17600 15.28800 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6811517E-02 1.1764594E-02 midg,1,midg; midg,igrid,midg -3.2124977E-04 4.1581523E-03 1,midg,midg; igrid,midg,midg -1.1196031E-02 -1.5080487E-03 gauss-seidel spectral radius is 0.9983197 estimated iterations to convergence 194 setup time was (sec) 0.5300000 now iterating at: 14:35:29 rms-change max change #iterations 3.403095 158.4339 at 10iterations 1.460528 53.54239 at 20iterations 0.6296427 23.82779 at 30iterations 0.2721864 10.22143 at 40iterations 0.1168631 4.308050 at 50iterations 5.0275777E-02 1.738144 at 60iterations 2.1639636E-02 0.7997408 at 70iterations 9.4009200E-03 0.3600140 at 80iterations 4.0348126E-03 0.1421347 at 90iterations 1.7400261E-03 6.4011097E-02 at 100iterations 7.5397990E-04 2.5644302E-02 at 110iterations 3.2595661E-04 1.2023926E-02 at 120iterations finished qdiffx linear iterations at : 14:35:36 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 3.2595661E-04 1.2023926E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:35:37 7.688u 0.194s 0:08.24 95.5% 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 14:35:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 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: 2.558779 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): -0.1650001 52.51700 ymin,ymax (A): -9.233000 39.80900 zmin,zma (A): -15.63700 46.97100 x,y,z range (A): 52.68200 49.04200 62.60800 scale (grids/A): 2.558779 object centre (A): 26.17600 15.28800 15.66700 number of atom coordinates read : 2693 total number of charged atoms : 2553 net assigned charge : 7.000018 assigned positive charge : 407.5164 centred at (gu) : 88.23218 91.54381 83.32248 assigned negative charge : -400.5174 centred at (gu) : 88.04601 91.10662 83.47587 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 144938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24919 grid for indexing accessible points = 1.400000 m= 67295 mr = 101707 m= 20026 mr = 52583 m= 3426 mr = 14839 m= 310 mr = 2079 m= 11 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 64681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20411 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) : 1.705852 object centre at (A) : 26.17600 15.28800 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.075599 0.1638437 midg,1,midg; midg,igrid,midg -1.5582065E-02 1.4984093E-02 1,midg,midg; igrid,midg,midg -0.1315428 -3.0558432E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.020000 now iterating at: 14:35:38 rms-change max change #iterations 8.747719 337.1763 at 10iterations 5.031788 134.4420 at 20iterations 2.877692 91.52556 at 30iterations 1.631598 40.45614 at 40iterations 0.9237453 21.88044 at 50iterations 0.5203875 12.71766 at 60iterations 0.2926228 7.062838 at 70iterations 0.1640676 3.355991 at 80iterations 9.1827713E-02 1.995926 at 90iterations 5.1460356E-02 1.048601 at 100iterations 2.8802691E-02 0.6177349 at 110iterations 1.6038967E-02 0.3792877 at 120iterations 8.9759119E-03 0.1808157 at 130iterations 5.0106244E-03 9.8665237E-02 at 140iterations 2.8025534E-03 5.6683540E-02 at 150iterations 1.5659337E-03 3.0363083E-02 at 160iterations 8.7814452E-04 1.9056320E-02 at 170iterations 4.9393863E-04 1.0393143E-02 at 180iterations finished qdiffx linear iterations at : 14:35:49 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 4.9393863E-04 1.0393143E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 14:35:50 12.388u 0.193s 0:12.85 97.8% 0+0k 0+0io 0pf+0w