Sat Oct 8 16:19:25 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 Sat Oct 8 2011 at 16:19:25 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 = 2356 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: 0.5828517 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): -2.148000 46.26700 ymin,ymax (A): -15.87200 29.92100 zmin,zma (A): -19.23900 41.84000 x,y,z range (A): 48.41500 45.79300 61.07900 scale (grids/A): 0.5828517 object centre (A): 22.05950 7.024500 11.30050 number of atom coordinates read : 2356 total number of charged atoms : 2275 net assigned charge : 3.000001 assigned positive charge : 349.7821 centred at (gu) : 90.26827 88.80064 88.81985 assigned negative charge : -346.7827 centred at (gu) : 90.28153 88.93785 88.86996 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5202 nv = 96 ne = 84 npr = 47936 no. pairs analyzed = 47936 no. exposed pairs = 2949 no. arc points = 20658 no. surface atoms = 1007 nbur = 1349 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 = 1.484000 m= 221 mr = 2752 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2700000 number of dielectric boundary points 2657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2096 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1278519E-09 -1.9827424E-10 midg,1,midg; midg,igrid,midg 4.2730903E-09 -1.4605738E-09 1,midg,midg; igrid,midg,midg 8.7133156E-10 4.5269505E-10 gauss-seidel spectral radius is 0.9847522 estimated iterations to convergence 66 setup time was (sec) 0.4900000 now iterating at: 16:19:26 rms-change max change #iterations 8.6329907E-02 17.12346 at 10iterations 6.9906944E-03 1.304083 at 20iterations 5.7869346E-04 9.0574265E-02 at 30iterations 6.9049718E-05 1.1802912E-02 at 40iterations 1.3453105E-05 2.6164055E-03 at 50iterations finished qdiffx linear iterations at : 16:19:28 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.3453105E-05 2.6164055E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 16:19:29 3.077u 0.137s 0:03.51 91.1% 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 16:19:29 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 = 2356 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: 1.748555 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): -2.148000 46.26700 ymin,ymax (A): -15.87200 29.92100 zmin,zma (A): -19.23900 41.84000 x,y,z range (A): 48.41500 45.79300 61.07900 scale (grids/A): 1.748555 object centre (A): 22.05950 7.024500 11.30050 number of atom coordinates read : 2356 total number of charged atoms : 2275 net assigned charge : 3.000001 assigned positive charge : 349.7821 centred at (gu) : 90.80456 86.40133 86.45908 assigned negative charge : -346.7827 centred at (gu) : 90.84427 86.81323 86.60986 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 57538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20658 grid for indexing accessible points = 1.400000 m= 18431 mr = 39301 m= 2301 mr = 13068 m= 67 mr = 1323 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 367 time to turn everything in is 0.4100000 number of dielectric boundary points 24631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17710 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) : 0.5828517 object centre at (A) : 22.05950 7.024500 11.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5510603E-02 1.1992523E-02 midg,1,midg; midg,igrid,midg 1.2617533E-02 -2.6487515E-03 1,midg,midg; igrid,midg,midg 1.3634594E-03 -1.5583973E-02 gauss-seidel spectral radius is 0.9983548 estimated iterations to convergence 196 setup time was (sec) 0.6700000 now iterating at: 16:19:30 rms-change max change #iterations 3.346401 181.6803 at 10iterations 1.456501 56.01167 at 20iterations 0.6346337 23.96571 at 30iterations 0.2773519 10.70920 at 40iterations 0.1209531 4.948761 at 50iterations 5.2734882E-02 1.833141 at 60iterations 2.2855645E-02 0.8355370 at 70iterations 9.9441977E-03 0.3672695 at 80iterations 4.3357275E-03 0.1652374 at 90iterations 1.8898909E-03 7.1645260E-02 at 100iterations 8.2742725E-04 3.0387878E-02 at 110iterations 3.6069661E-04 1.3425827E-02 at 120iterations finished qdiffx linear iterations at : 16:19:36 total time elapsed so far: 6.540000 # loops : 120 mean,max change (kT/e) : 3.6069661E-04 1.3425827E-02 energy calculations done at 6.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.740000 DelPhi exited at 16:19:36 6.740u 0.176s 0:07.28 94.9% 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 16:19:36 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 = 2356 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: 2.622833 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): -2.148000 46.26700 ymin,ymax (A): -15.87200 29.92100 zmin,zma (A): -19.23900 41.84000 x,y,z range (A): 48.41500 45.79300 61.07900 scale (grids/A): 2.622833 object centre (A): 22.05950 7.024500 11.30050 number of atom coordinates read : 2356 total number of charged atoms : 2275 net assigned charge : 3.000001 assigned positive charge : 349.7821 centred at (gu) : 91.20664 84.60190 84.68860 assigned negative charge : -346.7827 centred at (gu) : 91.26635 85.21982 84.91480 start vw surface at 0.1300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 133742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20658 grid for indexing accessible points = 1.400000 m= 62233 mr = 96121 m= 19787 mr = 49719 m= 3793 mr = 15633 m= 326 mr = 2725 m= 15 mr = 173 m= 0 mr = 7 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1353 time to turn everything in is 0.9600000 number of dielectric boundary points 55518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 18189 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) : 1.748555 object centre at (A) : 22.05950 7.024500 11.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1982228 0.4367416 midg,1,midg; midg,igrid,midg 0.1371761 -4.1968789E-02 1,midg,midg; igrid,midg,midg 2.7483858E-02 -0.2667155 gauss-seidel spectral radius is 0.9991737 estimated iterations to convergence 275 setup time was (sec) 1.230000 now iterating at: 16:19:38 rms-change max change #iterations 8.262869 337.8450 at 10iterations 4.683635 118.3599 at 20iterations 2.640545 56.76457 at 30iterations 1.485741 32.37689 at 40iterations 0.8338422 19.24208 at 50iterations 0.4676771 10.92945 at 60iterations 0.2619068 6.291313 at 70iterations 0.1465850 3.616608 at 80iterations 8.1594922E-02 1.896561 at 90iterations 4.5651123E-02 1.094816 at 100iterations 2.5465973E-02 0.5583792 at 110iterations 1.4196309E-02 0.3430395 at 120iterations 7.9018194E-03 0.1868916 at 130iterations 4.4133919E-03 0.1088815 at 140iterations 2.4642283E-03 5.1776886E-02 at 150iterations 1.3662839E-03 3.0931234E-02 at 160iterations 7.6596002E-04 1.7805099E-02 at 170iterations 4.2879526E-04 9.6852779E-03 at 180iterations finished qdiffx linear iterations at : 16:19:47 total time elapsed so far: 10.86000 # loops : 180 mean,max change (kT/e) : 4.2879526E-04 9.6852779E-03 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 16:19:48 11.026u 0.170s 0:11.48 97.4% 0+0k 0+0io 0pf+0w