Sat Oct 15 15:29:27 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 15 2011 at 15:29:27 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6621777 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): -27.76600 24.00300 ymin,ymax (A): -38.54000 15.22200 zmin,zma (A): -43.24400 6.531000 x,y,z range (A): 51.76900 53.76200 49.77500 scale (grids/A): 0.6621777 object centre (A): -1.881499 -11.65900 -18.35650 number of atom coordinates read : 2748 total number of charged atoms : 2612 net assigned charge : 7.451022 assigned positive charge : 425.8118 centred at (gu) : 91.92256 89.48489 90.24570 assigned negative charge : -418.3612 centred at (gu) : 91.97936 89.35303 90.04360 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8074 nv = 96 ne = 84 npr = 55293 no. pairs analyzed = 55293 no. exposed pairs = 3287 no. arc points = 23028 no. surface atoms = 1097 nbur = 1651 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4598 m= 6 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.4300000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4575552E-08 6.8216522E-08 midg,1,midg; midg,igrid,midg -1.0864480E-08 4.4596092E-08 1,midg,midg; igrid,midg,midg 2.2423666E-08 1.0741902E-08 gauss-seidel spectral radius is 0.9881902 estimated iterations to convergence 75 setup time was (sec) 0.7800000 now iterating at: 15:29:28 rms-change max change #iterations 0.1817495 26.66453 at 10iterations 1.9837499E-02 2.654897 at 20iterations 2.1367806E-03 0.3165285 at 30iterations 2.3339507E-04 3.0632019E-02 at 40iterations 3.0208786E-05 4.6138763E-03 at 50iterations finished qdiffx linear iterations at : 15:29:39 total time elapsed so far: 4.810000 # loops : 50 mean,max change (kT/e) : 3.0208786E-05 4.6138763E-03 energy calculations done at 4.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.030000 DelPhi exited at 15:29:39 5.034u 0.439s 0:12.35 44.2% 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 15 2011 at 15:29:39 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 1.986533 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): -27.76600 24.00300 ymin,ymax (A): -38.54000 15.22200 zmin,zma (A): -43.24400 6.531000 x,y,z range (A): 51.76900 53.76200 49.77500 scale (grids/A): 1.986533 object centre (A): -1.881499 -11.65900 -18.35650 number of atom coordinates read : 2748 total number of charged atoms : 2612 net assigned charge : 7.451022 assigned positive charge : 425.8118 centred at (gu) : 95.76720 88.45421 90.73703 assigned negative charge : -418.3612 centred at (gu) : 95.93785 88.05884 90.13045 start vw surface at 0.1500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 86341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23028 grid for indexing accessible points = 1.400000 m= 32203 mr = 60955 m= 5293 mr = 24218 m= 360 mr = 3379 m= 1 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 531 time to turn everything in is 0.8700000 number of dielectric boundary points 35505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 20648 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) : 0.6621777 object centre at (A) : -1.881499 -11.65900 -18.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0739597E-03 7.0793465E-02 midg,1,midg; midg,igrid,midg -3.1007862E-02 1.0427088E-02 1,midg,midg; igrid,midg,midg 5.6445699E-02 3.3347793E-02 gauss-seidel spectral radius is 0.9987531 estimated iterations to convergence 224 setup time was (sec) 1.270000 now iterating at: 15:29:42 rms-change max change #iterations 4.849064 225.1650 at 10iterations 2.336313 78.97549 at 20iterations 1.136567 36.20233 at 30iterations 0.5511677 16.00252 at 40iterations 0.2654902 8.489975 at 50iterations 0.1292965 3.652542 at 60iterations 6.2516451E-02 1.871141 at 70iterations 3.0272450E-02 0.9579010 at 80iterations 1.4666438E-02 0.4316187 at 90iterations 7.1097054E-03 0.2090549 at 100iterations 3.4500952E-03 0.1072845 at 110iterations 1.6797900E-03 4.8841476E-02 at 120iterations finished qdiffx linear iterations at : 15:29:55 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 1.6797900E-03 4.8841476E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 15:29:56 11.768u 0.533s 0:16.90 72.7% 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 Sat Oct 15 2011 at 15:29:56 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.979800 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): -27.76600 24.00300 ymin,ymax (A): -38.54000 15.22200 zmin,zma (A): -43.24400 6.531000 x,y,z range (A): 51.76900 53.76200 49.77500 scale (grids/A): 2.979800 object centre (A): -1.881499 -11.65900 -18.35650 number of atom coordinates read : 2748 total number of charged atoms : 2612 net assigned charge : 7.451022 assigned positive charge : 425.8118 centred at (gu) : 98.65077 87.68127 91.10529 assigned negative charge : -418.3612 centred at (gu) : 98.90678 87.08811 90.19563 start vw surface at 0.1700000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 199880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23028 grid for indexing accessible points = 1.400000 m= 103399 mr = 147332 m= 38400 mr = 85925 m= 9754 mr = 31264 m= 1534 mr = 7355 m= 131 mr = 1052 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 1636 time to turn everything in is 2.360000 number of dielectric boundary points 80107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.540000 number of grid points assigned charge 20896 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) : 1.986533 object centre at (A) : -1.881499 -11.65900 -18.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5282281E-02 0.7647606 midg,1,midg; midg,igrid,midg -0.4338535 0.1365380 1,midg,midg; igrid,midg,midg 0.4964163 0.4643718 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 2.780000 now iterating at: 15:29:59 rms-change max change #iterations 11.07196 405.8781 at 10iterations 6.490492 141.4998 at 20iterations 3.805599 72.11604 at 30iterations 2.221584 44.49144 at 40iterations 1.299855 25.11163 at 50iterations 0.7572538 13.08292 at 60iterations 0.4421113 7.503692 at 70iterations 0.2573666 4.231330 at 80iterations 0.1498660 2.583942 at 90iterations 8.7307699E-02 1.523294 at 100iterations 5.0694752E-02 0.9657822 at 110iterations 2.9499015E-02 0.4851761 at 120iterations 1.7160177E-02 0.2979507 at 130iterations 9.9751744E-03 0.1592350 at 140iterations 5.8170278E-03 9.1895103E-02 at 150iterations 3.3893934E-03 5.4868579E-02 at 160iterations 1.9813080E-03 3.1526566E-02 at 170iterations 1.1621540E-03 1.9953728E-02 at 180iterations finished qdiffx linear iterations at : 15:30:38 total time elapsed so far: 23.80000 # loops : 180 mean,max change (kT/e) : 1.1621540E-03 1.9953728E-02 energy calculations done at 23.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.00000 DelPhi exited at 15:30:39 24.008u 0.593s 0:42.46 57.9% 0+0k 0+0io 0pf+0w