Mon Oct 10 19:32:23 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 19:32:23 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 = 2629 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: 0.5933036 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): -0.8560000 48.91300 ymin,ymax (A): -17.43100 42.57200 zmin,zma (A): -12.08800 32.48700 x,y,z range (A): 49.76900 60.00300 44.57500 scale (grids/A): 0.5933036 object centre (A): 24.02850 12.57050 10.19950 number of atom coordinates read : 2629 total number of charged atoms : 2493 net assigned charge : 8.000023 assigned positive charge : 386.4715 centred at (gu) : 89.32812 91.26118 90.04282 assigned negative charge : -378.4723 centred at (gu) : 89.34527 91.20340 90.00552 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6185 nv = 96 ne = 84 npr = 52657 no. pairs analyzed = 52657 no. exposed pairs = 3560 no. arc points = 24936 no. surface atoms = 1195 nbur = 1434 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 = 1.456000 m= 309 mr = 3102 m= 1 mr = 19 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 0.2700000 number of dielectric boundary points 3374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2483 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6226790E-09 3.8231467E-09 midg,1,midg; midg,igrid,midg 8.0758994E-10 5.8253700E-09 1,midg,midg; igrid,midg,midg 3.7321479E-09 1.9186903E-09 gauss-seidel spectral radius is 0.9853086 estimated iterations to convergence 68 setup time was (sec) 0.5000000 now iterating at: 19:32:24 rms-change max change #iterations 9.9405736E-02 16.42811 at 10iterations 8.0550751E-03 1.297138 at 20iterations 6.8777101E-04 0.1219769 at 30iterations 7.0437804E-05 1.2321472E-02 at 40iterations 1.1631232E-05 2.7751923E-03 at 50iterations finished qdiffx linear iterations at : 19:32:26 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.1631232E-05 2.7751923E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 19:32:27 3.228u 0.196s 0:04.12 82.7% 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 19:32:27 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 = 2629 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.779911 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): -0.8560000 48.91300 ymin,ymax (A): -17.43100 42.57200 zmin,zma (A): -12.08800 32.48700 x,y,z range (A): 49.76900 60.00300 44.57500 scale (grids/A): 1.779911 object centre (A): 24.02850 12.57050 10.19950 number of atom coordinates read : 2629 total number of charged atoms : 2493 net assigned charge : 8.000023 assigned positive charge : 386.4715 centred at (gu) : 87.98372 93.78272 90.12769 assigned negative charge : -378.4723 centred at (gu) : 88.03559 93.60991 90.01610 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24936 grid for indexing accessible points = 1.400000 m= 22171 mr = 44025 m= 2819 mr = 15123 m= 118 mr = 1450 m= 0 mr = 27 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 194 time to turn everything in is 0.4900000 number of dielectric boundary points 31183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19436 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) : 0.5933036 object centre at (A) : 24.02850 12.57050 10.19950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3189636E-03 1.3813095E-02 midg,1,midg; midg,igrid,midg -4.8950984E-04 -7.9422183E-03 1,midg,midg; igrid,midg,midg 2.6628394E-02 1.1451107E-02 gauss-seidel spectral radius is 0.9984502 estimated iterations to convergence 202 setup time was (sec) 0.7900000 now iterating at: 19:32:28 rms-change max change #iterations 3.651402 172.6525 at 10iterations 1.617727 60.75567 at 20iterations 0.7203125 24.12251 at 30iterations 0.3221409 10.59159 at 40iterations 0.1426877 5.249452 at 50iterations 6.3794792E-02 2.470800 at 60iterations 2.8345991E-02 0.9745941 at 70iterations 1.2600950E-02 0.4569201 at 80iterations 5.6219962E-03 0.2054939 at 90iterations 2.5001669E-03 0.1150706 at 100iterations 1.1200084E-03 4.0548325E-02 at 110iterations 5.0224212E-04 2.0519257E-02 at 120iterations finished qdiffx linear iterations at : 19:32:35 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 5.0224212E-04 2.0519257E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 19:32:35 7.513u 0.253s 0:08.10 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 Mon Oct 10 2011 at 19:32:35 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 = 2629 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: 2.669866 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): -0.8560000 48.91300 ymin,ymax (A): -17.43100 42.57200 zmin,zma (A): -12.08800 32.48700 x,y,z range (A): 49.76900 60.00300 44.57500 scale (grids/A): 2.669866 object centre (A): 24.02850 12.57050 10.19950 number of atom coordinates read : 2629 total number of charged atoms : 2493 net assigned charge : 8.000023 assigned positive charge : 386.4715 centred at (gu) : 86.97536 95.67389 90.19131 assigned negative charge : -378.4723 centred at (gu) : 87.05327 95.41478 90.02409 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 154473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24936 grid for indexing accessible points = 1.400000 m= 73304 mr = 107794 m= 23680 mr = 57344 m= 4688 mr = 17899 m= 527 mr = 3106 m= 13 mr = 282 m= 0 mr = 2 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 626 time to turn everything in is 1.190000 number of dielectric boundary points 70258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19936 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) : 1.779911 object centre at (A) : 24.02850 12.57050 10.19950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9263302E-02 0.1589084 midg,1,midg; midg,igrid,midg 7.7720210E-02 -5.4371182E-02 1,midg,midg; igrid,midg,midg 0.3645088 9.8219775E-02 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 1.510000 now iterating at: 19:32:37 rms-change max change #iterations 9.034779 320.5399 at 10iterations 5.247492 129.5817 at 20iterations 3.025075 69.35639 at 30iterations 1.729418 39.47582 at 40iterations 0.9884545 22.08553 at 50iterations 0.5635667 13.17634 at 60iterations 0.3199818 7.134858 at 70iterations 0.1818004 3.405921 at 80iterations 0.1031617 2.262791 at 90iterations 5.8417641E-02 1.295092 at 100iterations 3.3101242E-02 0.6810895 at 110iterations 1.8763131E-02 0.3949814 at 120iterations 1.0610904E-02 0.2062627 at 130iterations 5.9913853E-03 0.1350017 at 140iterations 3.3909443E-03 7.0795059E-02 at 150iterations 1.9176599E-03 3.6972046E-02 at 160iterations 1.0855482E-03 2.3265839E-02 at 170iterations 6.1344606E-04 1.2729645E-02 at 180iterations finished qdiffx linear iterations at : 19:32:48 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 6.1344606E-04 1.2729645E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 19:32:49 12.199u 0.279s 0:13.32 93.5% 0+0k 0+0io 0pf+0w