Sat Oct 8 16:28:13 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 8 2011 at 16:28:13 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6667041 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): -2.119000 47.63600 ymin,ymax (A): -17.75300 28.83400 zmin,zma (A): -18.13700 35.26000 x,y,z range (A): 49.75500 46.58700 53.39700 scale (grids/A): 0.6667041 object centre (A): 22.75850 5.540500 8.561502 number of atom coordinates read : 2270 total number of charged atoms : 2186 net assigned charge : 3.000000 assigned positive charge : 336.3272 centred at (gu) : 89.92667 89.26948 90.06950 assigned negative charge : -333.3279 centred at (gu) : 89.98203 89.40889 90.14503 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6697 nv = 96 ne = 84 npr = 46663 no. pairs analyzed = 46663 no. exposed pairs = 2831 no. arc points = 19272 no. surface atoms = 970 nbur = 1300 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 432 mr = 3746 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1782 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3685883E-08 -6.5157542E-09 midg,1,midg; midg,igrid,midg 4.2629026E-08 -1.6727764E-08 1,midg,midg; igrid,midg,midg 2.0319863E-08 -2.2486804E-09 gauss-seidel spectral radius is 0.9883068 estimated iterations to convergence 75 setup time was (sec) 0.6400000 now iterating at: 16:28:14 rms-change max change #iterations 0.1623299 25.40075 at 10iterations 1.7974528E-02 2.410433 at 20iterations 2.0286336E-03 0.3095112 at 30iterations 2.8892569E-04 4.1790009E-02 at 40iterations 6.0957769E-05 9.3407631E-03 at 50iterations finished qdiffx linear iterations at : 16:28:19 total time elapsed so far: 5.510000 # loops : 50 mean,max change (kT/e) : 6.0957769E-05 9.3407631E-03 energy calculations done at 5.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 16:28:19 5.687u 0.432s 0:06.41 95.3% 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 8 2011 at 16:28:20 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.000112 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): -2.119000 47.63600 ymin,ymax (A): -17.75300 28.83400 zmin,zma (A): -18.13700 35.26000 x,y,z range (A): 49.75500 46.58700 53.39700 scale (grids/A): 2.000112 object centre (A): 22.75850 5.540500 8.561502 number of atom coordinates read : 2270 total number of charged atoms : 2186 net assigned charge : 3.000000 assigned positive charge : 336.3272 centred at (gu) : 89.77978 87.80769 90.20832 assigned negative charge : -333.3279 centred at (gu) : 89.94597 88.22656 90.43516 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19272 grid for indexing accessible points = 1.400000 m= 27196 mr = 49828 m= 5369 mr = 20329 m= 387 mr = 3697 m= 10 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 390 time to turn everything in is 0.6100000 number of dielectric boundary points 30514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17276 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) : 0.6667041 object centre at (A) : 22.75850 5.540500 8.561502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0478694E-02 -8.2315765E-03 midg,1,midg; midg,igrid,midg 2.2818161E-02 -7.9165166E-03 1,midg,midg; igrid,midg,midg 1.0369610E-02 -3.7905242E-02 gauss-seidel spectral radius is 0.9987206 estimated iterations to convergence 221 setup time was (sec) 1.010000 now iterating at: 16:28:21 rms-change max change #iterations 4.313221 172.9370 at 10iterations 2.069185 80.90002 at 20iterations 0.9916450 33.44022 at 30iterations 0.4758908 16.14577 at 40iterations 0.2291715 7.183030 at 50iterations 0.1097768 3.579723 at 60iterations 5.2671496E-02 1.692153 at 70iterations 2.5327828E-02 0.7928839 at 80iterations 1.2179704E-02 0.4331512 at 90iterations 5.8794562E-03 0.1829376 at 100iterations 2.8248604E-03 8.3978653E-02 at 110iterations 1.3696830E-03 4.1168213E-02 at 120iterations finished qdiffx linear iterations at : 16:28:33 total time elapsed so far: 12.84000 # loops : 120 mean,max change (kT/e) : 1.3696830E-03 4.1168213E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 16:28:33 13.006u 0.531s 0:13.80 98.0% 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 Sat Oct 8 2011 at 16:28:33 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.000168 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): -2.119000 47.63600 ymin,ymax (A): -17.75300 28.83400 zmin,zma (A): -18.13700 35.26000 x,y,z range (A): 49.75500 46.58700 53.39700 scale (grids/A): 3.000168 object centre (A): 22.75850 5.540500 8.561502 number of atom coordinates read : 2270 total number of charged atoms : 2186 net assigned charge : 3.000000 assigned positive charge : 336.3272 centred at (gu) : 89.66966 86.71149 90.31236 assigned negative charge : -333.3279 centred at (gu) : 89.91890 87.33987 90.65268 start vw surface at 0.1000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 165551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19272 grid for indexing accessible points = 1.400000 m= 84995 mr = 120916 m= 34584 mr = 69660 m= 10151 mr = 28414 m= 1667 mr = 8058 m= 99 mr = 1096 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1350 time to turn everything in is 1.700000 number of dielectric boundary points 68867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 17488 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) : 2.000112 object centre at (A) : 22.75850 5.540500 8.561502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2901607 -3.4254007E-02 midg,1,midg; midg,igrid,midg 0.1511813 -0.1027587 1,midg,midg; igrid,midg,midg 0.1315868 -0.4827263 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 2.080000 now iterating at: 16:28:36 rms-change max change #iterations 9.978434 375.7261 at 10iterations 5.867932 127.9381 at 20iterations 3.445000 71.86100 at 30iterations 2.021146 47.58840 at 40iterations 1.178829 22.94831 at 50iterations 0.6860320 12.21892 at 60iterations 0.3993410 7.641317 at 70iterations 0.2325081 4.216669 at 80iterations 0.1349396 2.713177 at 90iterations 7.8175217E-02 1.324037 at 100iterations 4.5338679E-02 0.7957420 at 110iterations 2.6302002E-02 0.4806843 at 120iterations 1.5243799E-02 0.2719479 at 130iterations 8.8252155E-03 0.1748579 at 140iterations 5.1176287E-03 9.0689659E-02 at 150iterations 2.9844947E-03 5.2551270E-02 at 160iterations 1.7436669E-03 3.2787323E-02 at 170iterations 1.0263643E-03 1.8205643E-02 at 180iterations finished qdiffx linear iterations at : 16:28:56 total time elapsed so far: 21.66000 # loops : 180 mean,max change (kT/e) : 1.0263643E-03 1.8205643E-02 energy calculations done at 21.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.83000 DelPhi exited at 16:28:56 21.834u 0.565s 0:22.69 98.6% 0+0k 0+0io 0pf+0w