Tue Oct 11 08:21:34 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 Tue Oct 11 2011 at 08:21:34 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1179 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7428584 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): -6.468000 32.34900 ymin,ymax (A): 1.098000 40.57000 zmin,zma (A): -1.639000 46.28400 x,y,z range (A): 38.81700 39.47200 47.92300 scale (grids/A): 0.7428584 object centre (A): 12.94050 20.83400 22.32250 number of atom coordinates read : 1179 total number of charged atoms : 1052 net assigned charge : 5.514003 assigned positive charge : 176.5951 centred at (gu) : 88.72585 89.11514 88.68591 assigned negative charge : -171.0812 centred at (gu) : 88.43015 89.09042 88.69374 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4519 nv = 96 ne = 84 npr = 23046 no. pairs analyzed = 23046 no. exposed pairs = 1488 no. arc points = 11216 no. surface atoms = 499 nbur = 680 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 2385 m= 0 mr = 49 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.1200000 number of dielectric boundary points 2392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 900 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 4485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3997793E-07 8.0170395E-08 midg,1,midg; midg,igrid,midg 1.0728028E-07 1.0222740E-07 1,midg,midg; igrid,midg,midg -8.9692207E-08 2.1361579E-07 gauss-seidel spectral radius is 0.9904625 estimated iterations to convergence 83 setup time was (sec) 0.3100000 now iterating at: 08:21:34 rms-change max change #iterations 0.1775221 32.26665 at 10iterations 2.3736106E-02 3.699451 at 20iterations 3.2334002E-03 0.5625267 at 30iterations 4.1904690E-04 6.7082405E-02 at 40iterations 5.6415174E-05 9.2926025E-03 at 50iterations finished qdiffx linear iterations at : 08:21:37 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.6415174E-05 9.2926025E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:21:38 3.320u 0.164s 0:04.05 85.9% 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 Tue Oct 11 2011 at 08:21:38 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1179 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.228575 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): -6.468000 32.34900 ymin,ymax (A): 1.098000 40.57000 zmin,zma (A): -1.639000 46.28400 x,y,z range (A): 38.81700 39.47200 47.92300 scale (grids/A): 2.228575 object centre (A): 12.94050 20.83400 22.32250 number of atom coordinates read : 1179 total number of charged atoms : 1052 net assigned charge : 5.514003 assigned positive charge : 176.5951 centred at (gu) : 86.17783 87.34549 86.05798 assigned negative charge : -171.0812 centred at (gu) : 85.29055 87.27141 86.08153 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 46794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11216 grid for indexing accessible points = 1.400000 m= 18290 mr = 30545 m= 3841 mr = 13881 m= 414 mr = 2670 m= 20 mr = 242 m= 0 mr = 12 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 411 time to turn everything in is 0.2700000 number of dielectric boundary points 22009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8390 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) : 0.7428584 object centre at (A) : 12.94050 20.83400 22.32250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8462250E-02 5.1445616E-03 midg,1,midg; midg,igrid,midg 3.7770625E-02 3.2767750E-02 1,midg,midg; igrid,midg,midg -2.8072251E-02 4.1013610E-02 gauss-seidel spectral radius is 0.9988437 estimated iterations to convergence 233 setup time was (sec) 0.4800000 now iterating at: 08:21:39 rms-change max change #iterations 3.655411 264.2507 at 10iterations 1.816534 81.82966 at 20iterations 0.9026502 42.00502 at 30iterations 0.4479483 15.84290 at 40iterations 0.2213294 9.870533 at 50iterations 0.1104961 4.241163 at 60iterations 5.4455195E-02 1.965950 at 70iterations 2.7058400E-02 0.9286652 at 80iterations 1.3419287E-02 0.4839191 at 90iterations 6.6669020E-03 0.2443504 at 100iterations 3.3079297E-03 0.1318989 at 110iterations 1.6421104E-03 6.1244965E-02 at 120iterations finished qdiffx linear iterations at : 08:21:46 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.6421104E-03 6.1244965E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 08:21:46 7.622u 0.229s 0:08.18 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 Tue Oct 11 2011 at 08:21:46 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1179 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.342862 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): -6.468000 32.34900 ymin,ymax (A): 1.098000 40.57000 zmin,zma (A): -1.639000 46.28400 x,y,z range (A): 38.81700 39.47200 47.92300 scale (grids/A): 3.342862 object centre (A): 12.94050 20.83400 22.32250 number of atom coordinates read : 1179 total number of charged atoms : 1052 net assigned charge : 5.514003 assigned positive charge : 176.5951 centred at (gu) : 84.26668 86.01817 84.08689 assigned negative charge : -171.0812 centred at (gu) : 82.93594 85.90711 84.12237 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 107740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11216 grid for indexing accessible points = 1.400000 m= 55565 mr = 73994 m= 23646 mr = 45619 m= 7379 mr = 19680 m= 1662 mr = 5880 m= 263 mr = 1304 m= 41 mr = 204 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1640 time to turn everything in is 0.7600000 number of dielectric boundary points 49577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 8416 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) : 2.228575 object centre at (A) : 12.94050 20.83400 22.32250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2755992 5.5245787E-02 midg,1,midg; midg,igrid,midg 0.3372600 0.2787847 1,midg,midg; igrid,midg,midg -0.2226846 0.3034788 gauss-seidel spectral radius is 0.9992942 estimated iterations to convergence 297 setup time was (sec) 0.9800000 now iterating at: 08:21:47 rms-change max change #iterations 8.036654 287.1159 at 10iterations 4.696296 128.9210 at 20iterations 2.724210 65.03390 at 30iterations 1.577139 37.18178 at 40iterations 0.9184886 19.95021 at 50iterations 0.5314007 11.30717 at 60iterations 0.3071978 6.283442 at 70iterations 0.1789241 3.862206 at 80iterations 0.1036526 2.246416 at 90iterations 6.0157970E-02 1.274435 at 100iterations 3.4825172E-02 0.7680321 at 110iterations 2.0211725E-02 0.4290428 at 120iterations 1.1710402E-02 0.2522612 at 130iterations 6.8075596E-03 0.1529331 at 140iterations 3.9505945E-03 8.1964493E-02 at 150iterations 2.2931434E-03 4.9520493E-02 at 160iterations 1.3283715E-03 2.9190063E-02 at 170iterations 7.7224121E-04 1.6996384E-02 at 180iterations finished qdiffx linear iterations at : 08:21:58 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 7.7224121E-04 1.6996384E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 08:21:59 12.223u 0.251s 0:12.79 97.4% 0+0k 0+0io 0pf+0w