Tue Oct 11 03:48:35 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 Tue Oct 11 2011 at 03:48:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6525405 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): -10.96700 36.50500 ymin,ymax (A): -27.01700 21.72400 zmin,zma (A): -9.001000 45.55500 x,y,z range (A): 47.47200 48.74100 54.55600 scale (grids/A): 0.6525405 object centre (A): 12.76900 -2.646501 18.27700 number of atom coordinates read : 2833 total number of charged atoms : 2679 net assigned charge : 1.162013 assigned positive charge : 427.8696 centred at (gu) : 89.91047 90.61706 91.33678 assigned negative charge : -426.7082 centred at (gu) : 89.62398 90.51849 91.26949 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8093 nv = 96 ne = 84 npr = 56939 no. pairs analyzed = 56939 no. exposed pairs = 3495 no. arc points = 24492 no. surface atoms = 1174 nbur = 1659 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4613 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3100000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2289 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4064364E-09 1.8916669E-08 midg,1,midg; midg,igrid,midg -1.3641738E-08 2.2486914E-08 1,midg,midg; igrid,midg,midg -5.1631474E-08 5.1002111E-08 gauss-seidel spectral radius is 0.9878489 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 03:48:36 rms-change max change #iterations 0.1656602 24.99404 at 10iterations 1.7524024E-02 2.382071 at 20iterations 1.9406729E-03 0.2629318 at 30iterations 2.5007053E-04 4.1084290E-02 at 40iterations 4.6948720E-05 7.1697235E-03 at 50iterations finished qdiffx linear iterations at : 03:48:38 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 4.6948720E-05 7.1697235E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 03:48:39 3.121u 0.125s 0:03.80 85.2% 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 Tue Oct 11 2011 at 03:48:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.957622 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): -10.96700 36.50500 ymin,ymax (A): -27.01700 21.72400 zmin,zma (A): -9.001000 45.55500 x,y,z range (A): 47.47200 48.74100 54.55600 scale (grids/A): 1.957622 object centre (A): 12.76900 -2.646501 18.27700 number of atom coordinates read : 2833 total number of charged atoms : 2679 net assigned charge : 1.162013 assigned positive charge : 427.8696 centred at (gu) : 89.73080 91.85083 94.00972 assigned negative charge : -426.7082 centred at (gu) : 88.87151 91.55499 93.80804 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 86531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24492 grid for indexing accessible points = 1.400000 m= 33087 mr = 60842 m= 5583 mr = 25157 m= 338 mr = 3681 m= 5 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2442 time to turn everything in is 0.6200000 number of dielectric boundary points 35743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 21154 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) : 0.6525405 object centre at (A) : 12.76900 -2.646501 18.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6732515E-02 7.4220244E-03 midg,1,midg; midg,igrid,midg -1.2955066E-02 3.8744756E-03 1,midg,midg; igrid,midg,midg -1.5914613E-02 6.2797889E-02 gauss-seidel spectral radius is 0.9987305 estimated iterations to convergence 222 setup time was (sec) 0.8800000 now iterating at: 03:48:40 rms-change max change #iterations 4.732916 225.3469 at 10iterations 2.272607 90.58142 at 20iterations 1.097402 30.07443 at 30iterations 0.5289994 17.90797 at 40iterations 0.2553525 7.495366 at 50iterations 0.1233560 3.463326 at 60iterations 5.9483860E-02 1.631836 at 70iterations 2.8618604E-02 0.7777863 at 80iterations 1.3815117E-02 0.4194374 at 90iterations 6.6911289E-03 0.1813231 at 100iterations 3.2226762E-03 9.2046738E-02 at 110iterations 1.5579237E-03 4.7456741E-02 at 120iterations finished qdiffx linear iterations at : 03:48:46 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 1.5579237E-03 4.7456741E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.140000 DelPhi exited at 03:48:47 7.142u 0.170s 0:07.88 92.7% 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 Tue Oct 11 2011 at 03:48:47 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.936432 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): -10.96700 36.50500 ymin,ymax (A): -27.01700 21.72400 zmin,zma (A): -9.001000 45.55500 x,y,z range (A): 47.47200 48.74100 54.55600 scale (grids/A): 2.936432 object centre (A): 12.76900 -2.646501 18.27700 number of atom coordinates read : 2833 total number of charged atoms : 2679 net assigned charge : 1.162013 assigned positive charge : 427.8696 centred at (gu) : 89.59592 92.77625 96.01456 assigned negative charge : -426.7082 centred at (gu) : 88.30726 92.33230 95.71191 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 199569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24492 grid for indexing accessible points = 1.400000 m= 105371 mr = 146751 m= 40377 mr = 87596 m= 10299 mr = 33235 m= 1583 mr = 7934 m= 112 mr = 1131 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 8224 time to turn everything in is 1.520000 number of dielectric boundary points 80621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 21430 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) : 1.957622 object centre at (A) : 12.76900 -2.646501 18.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6443386 0.3129475 midg,1,midg; midg,igrid,midg -0.1696678 3.7418045E-02 1,midg,midg; igrid,midg,midg -8.7946624E-02 0.5363643 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 1.820000 now iterating at: 03:48:49 rms-change max change #iterations 10.95677 516.6486 at 10iterations 6.467072 153.1569 at 20iterations 3.813405 90.35555 at 30iterations 2.244619 38.13873 at 40iterations 1.316069 26.62728 at 50iterations 0.7692715 17.14743 at 60iterations 0.4505450 8.157050 at 70iterations 0.2625184 4.726125 at 80iterations 0.1532761 2.729546 at 90iterations 8.9376584E-02 1.553413 at 100iterations 5.2136242E-02 0.8355026 at 110iterations 3.0365450E-02 0.5107312 at 120iterations 1.7689819E-02 0.2832041 at 130iterations 1.0348850E-02 0.1802177 at 140iterations 6.0586235E-03 9.9399567E-02 at 150iterations 3.5637373E-03 6.7169189E-02 at 160iterations 2.1124289E-03 3.6987305E-02 at 170iterations 1.2721965E-03 2.7591705E-02 at 180iterations finished qdiffx linear iterations at : 03:48:58 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 1.2721965E-03 2.7591705E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 03:48:59 11.753u 0.204s 0:12.24 97.6% 0+0k 0+0io 0pf+0w