Sat Oct 15 14:49:45 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 14:49:46 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 !!! WARNING: HIT 6 has a net charge of 0.5140 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7474595 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): 34.69100 82.31900 ymin,ymax (A): 11.20100 52.59000 zmin,zma (A): 25.65700 60.60500 x,y,z range (A): 47.62800 41.38900 34.94801 scale (grids/A): 0.7474595 object centre (A): 58.50500 31.89550 43.13100 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.04199 assigned positive charge : 214.9342 centred at (gu) : 90.39258 90.32790 88.67767 assigned negative charge : -198.8922 centred at (gu) : 90.52132 90.23903 88.64009 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4863 nv = 96 ne = 84 npr = 27562 no. pairs analyzed = 27562 no. exposed pairs = 1622 no. arc points = 12070 no. surface atoms = 555 nbur = 806 mkacc time = 6.0000010E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 2528 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1900000 number of dielectric boundary points 2607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1100 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 5220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8550147E-07 2.8406757E-07 midg,1,midg; midg,igrid,midg 2.5145144E-07 4.2075885E-07 1,midg,midg; igrid,midg,midg 3.9606735E-07 2.5320378E-07 gauss-seidel spectral radius is 0.9905868 estimated iterations to convergence 84 setup time was (sec) 0.4000000 now iterating at: 14:49:46 rms-change max change #iterations 0.2110184 34.13232 at 10iterations 2.8368125E-02 5.802982 at 20iterations 3.8144772E-03 0.6013489 at 30iterations 5.2300142E-04 0.1021814 at 40iterations 7.0512513E-05 1.1709213E-02 at 50iterations finished qdiffx linear iterations at : 14:49:49 total time elapsed so far: 2.820000 # loops : 50 mean,max change (kT/e) : 7.0512513E-05 1.1709213E-02 energy calculations done at 2.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 14:49:49 2.999u 0.164s 0:03.45 91.3% 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 15 2011 at 14:49:49 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 !!! WARNING: HIT 6 has a net charge of 0.5140 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.242378 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): 34.69100 82.31900 ymin,ymax (A): 11.20100 52.59000 zmin,zma (A): 25.65700 60.60500 x,y,z range (A): 47.62800 41.38900 34.94801 scale (grids/A): 2.242378 object centre (A): 58.50500 31.89550 43.13100 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.04199 assigned positive charge : 214.9342 centred at (gu) : 91.17798 90.98380 86.03310 assigned negative charge : -198.8922 centred at (gu) : 91.56413 90.71739 85.92046 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 50886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12070 grid for indexing accessible points = 1.400000 m= 18805 mr = 33678 m= 4214 mr = 13865 m= 552 mr = 2897 m= 24 mr = 357 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 469 time to turn everything in is 0.3900000 number of dielectric boundary points 23677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9857 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) : 0.7474595 object centre at (A) : 58.50500 31.89550 43.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2715853E-02 2.9506480E-02 midg,1,midg; midg,igrid,midg 2.6672183E-02 8.9657582E-02 1,midg,midg; igrid,midg,midg 0.1303174 0.1072174 gauss-seidel spectral radius is 0.9988628 estimated iterations to convergence 235 setup time was (sec) 0.6500000 now iterating at: 14:49:50 rms-change max change #iterations 4.039805 182.8716 at 10iterations 2.012114 83.01786 at 20iterations 1.004419 34.36179 at 30iterations 0.5013770 17.53421 at 40iterations 0.2504978 9.281792 at 50iterations 0.1254758 4.512812 at 60iterations 6.2306907E-02 2.163593 at 70iterations 3.1240674E-02 1.181173 at 80iterations 1.5538226E-02 0.5301037 at 90iterations 7.7713076E-03 0.2741776 at 100iterations 3.8810305E-03 0.1390038 at 110iterations 1.9326318E-03 6.9808960E-02 at 120iterations finished qdiffx linear iterations at : 14:49:56 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 1.9326318E-03 6.9808960E-02 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.660000 DelPhi exited at 14:49:56 6.659u 0.189s 0:07.19 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 15 2011 at 14:49:56 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 !!! WARNING: HIT 6 has a net charge of 0.5140 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 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: 3.363568 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): 34.69100 82.31900 ymin,ymax (A): 11.20100 52.59000 zmin,zma (A): 25.65700 60.60500 x,y,z range (A): 47.62800 41.38900 34.94801 scale (grids/A): 3.363568 object centre (A): 58.50500 31.89550 43.13100 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.04199 assigned positive charge : 214.9342 centred at (gu) : 91.76704 91.47567 84.04964 assigned negative charge : -198.8922 centred at (gu) : 92.34618 91.07606 83.88079 start vw surface at 0.1000000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 117217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12070 grid for indexing accessible points = 1.400000 m= 58339 mr = 81379 m= 24224 mr = 47446 m= 8248 mr = 19742 m= 2091 mr = 6489 m= 356 mr = 1630 m= 20 mr = 266 m= 0 mr = 13 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1639 time to turn everything in is 1.210000 number of dielectric boundary points 53530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 9904 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) : 2.242378 object centre at (A) : 58.50500 31.89550 43.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3554966 0.1563348 midg,1,midg; midg,igrid,midg 0.1219682 0.7530811 1,midg,midg; igrid,midg,midg 1.042088 0.8203920 gauss-seidel spectral radius is 0.9992984 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 14:49:58 rms-change max change #iterations 8.822487 239.0222 at 10iterations 5.148122 128.5468 at 20iterations 3.000992 63.97909 at 30iterations 1.749633 34.71301 at 40iterations 1.018560 22.53979 at 50iterations 0.5923693 12.03116 at 60iterations 0.3445924 7.165133 at 70iterations 0.2000241 3.829560 at 80iterations 0.1163879 2.382690 at 90iterations 6.7770302E-02 1.415411 at 100iterations 3.9475661E-02 0.8685309 at 110iterations 2.2920184E-02 0.4586983 at 120iterations 1.3372102E-02 0.2656372 at 130iterations 7.7709388E-03 0.1511612 at 140iterations 4.5302911E-03 9.4469070E-02 at 150iterations 2.6286815E-03 5.0773144E-02 at 160iterations 1.5311860E-03 3.0242324E-02 at 170iterations 8.8819308E-04 1.8331528E-02 at 180iterations finished qdiffx linear iterations at : 14:50:07 total time elapsed so far: 10.79000 # loops : 180 mean,max change (kT/e) : 8.8819308E-04 1.8331528E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 14:50:08 10.969u 0.174s 0:11.46 97.1% 0+0k 0+0io 0pf+0w