Sat Oct 8 20:43:37 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 20:43:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 457 has a net charge of 1.4000 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: 0.6501095 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): -31.77500 17.46900 ymin,ymax (A): -23.14900 23.30000 zmin,zma (A): -12.45600 42.30400 x,y,z range (A): 49.24400 46.44900 54.76000 scale (grids/A): 0.6501095 object centre (A): -7.153000 7.5499535E-02 14.92400 number of atom coordinates read : 2517 total number of charged atoms : 2389 net assigned charge : 2.500009 assigned positive charge : 380.8313 centred at (gu) : 88.57903 89.02258 90.12807 assigned negative charge : -378.3316 centred at (gu) : 88.45597 89.05125 90.06016 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7068 nv = 96 ne = 84 npr = 52267 no. pairs analyzed = 52267 no. exposed pairs = 2898 no. arc points = 20986 no. surface atoms = 980 nbur = 1537 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 4045 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.3800000 number of dielectric boundary points 3375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2010 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9454885E-09 1.5512846E-08 midg,1,midg; midg,igrid,midg 1.1455572E-08 6.9625455E-10 1,midg,midg; igrid,midg,midg -1.8444192E-08 1.7142384E-08 gauss-seidel spectral radius is 0.9877295 estimated iterations to convergence 74 setup time was (sec) 0.6700000 now iterating at: 20:43:38 rms-change max change #iterations 0.1558719 20.70834 at 10iterations 1.6048687E-02 2.218175 at 20iterations 1.6164317E-03 0.2104111 at 30iterations 1.7039060E-04 2.1561146E-02 at 40iterations 1.7770475E-05 2.8305054E-03 at 50iterations finished qdiffx linear iterations at : 20:43:42 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.7770475E-05 2.8305054E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.880000 DelPhi exited at 20:43:43 4.880u 0.495s 0:05.70 94.2% 0+0k 0+0io 5pf+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 20:43:43 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 457 has a net charge of 1.4000 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: 1.950329 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): -31.77500 17.46900 ymin,ymax (A): -23.14900 23.30000 zmin,zma (A): -12.45600 42.30400 x,y,z range (A): 49.24400 46.44900 54.76000 scale (grids/A): 1.950329 object centre (A): -7.153000 7.5499535E-02 14.92400 number of atom coordinates read : 2517 total number of charged atoms : 2389 net assigned charge : 2.500009 assigned positive charge : 380.8313 centred at (gu) : 85.73671 87.06725 90.38403 assigned negative charge : -378.3316 centred at (gu) : 85.36782 87.15372 90.18033 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 76505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 27753 mr = 54066 m= 4447 mr = 20839 m= 249 mr = 2834 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 6528 time to turn everything in is 0.7800000 number of dielectric boundary points 31133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 18813 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) : 0.6501095 object centre at (A) : -7.153000 7.5499535E-02 14.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2536267E-02 1.4338205E-03 midg,1,midg; midg,igrid,midg 1.6176298E-02 9.3906443E-04 1,midg,midg; igrid,midg,midg -2.9999865E-03 4.4424176E-02 gauss-seidel spectral radius is 0.9986867 estimated iterations to convergence 219 setup time was (sec) 1.140000 now iterating at: 20:43:44 rms-change max change #iterations 4.361362 173.9821 at 10iterations 2.078830 66.32190 at 20iterations 0.9874889 32.13410 at 30iterations 0.4695359 17.06708 at 40iterations 0.2228418 7.167782 at 50iterations 0.1062096 3.341290 at 60iterations 5.0491273E-02 1.637977 at 70iterations 2.4006482E-02 0.7394462 at 80iterations 1.1416896E-02 0.3476982 at 90iterations 5.4230499E-03 0.1848516 at 100iterations 2.5782411E-03 8.1882477E-02 at 110iterations 1.2312552E-03 3.6911011E-02 at 120iterations finished qdiffx linear iterations at : 20:43:55 total time elapsed so far: 11.80000 # loops : 120 mean,max change (kT/e) : 1.2312552E-03 3.6911011E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 20:43:56 12.014u 0.525s 0:12.82 97.7% 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 8 2011 at 20:43:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 457 has a net charge of 1.4000 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: 2.925493 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): -31.77500 17.46900 ymin,ymax (A): -23.14900 23.30000 zmin,zma (A): -12.45600 42.30400 x,y,z range (A): 49.24400 46.44900 54.76000 scale (grids/A): 2.925493 object centre (A): -7.153000 7.5499535E-02 14.92400 number of atom coordinates read : 2517 total number of charged atoms : 2389 net assigned charge : 2.500009 assigned positive charge : 380.8313 centred at (gu) : 83.60491 85.60084 90.57587 assigned negative charge : -378.3316 centred at (gu) : 83.05169 85.73064 90.27046 start vw surface at 0.1700000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 176772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 90230 mr = 130441 m= 32747 mr = 74835 m= 7900 mr = 26497 m= 1101 mr = 6063 m= 67 mr = 731 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 22606 time to turn everything in is 2.050000 number of dielectric boundary points 70222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 19112 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) : 1.950329 object centre at (A) : -7.153000 7.5499535E-02 14.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1203114 -4.9476512E-03 midg,1,midg; midg,igrid,midg 0.1649318 -5.3934369E-02 1,midg,midg; igrid,midg,midg 3.1941578E-02 0.5141958 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 2.430000 now iterating at: 20:43:59 rms-change max change #iterations 10.04567 383.8423 at 10iterations 5.822647 131.1633 at 20iterations 3.364534 64.08601 at 30iterations 1.943380 42.45111 at 40iterations 1.124871 19.69045 at 50iterations 0.6489678 13.62551 at 60iterations 0.3734453 8.463320 at 70iterations 0.2157129 4.052525 at 80iterations 0.1239082 2.082325 at 90iterations 7.1492158E-02 1.217323 at 100iterations 4.1246850E-02 0.7625089 at 110iterations 2.3689333E-02 0.4622345 at 120iterations 1.3630684E-02 0.2302647 at 130iterations 7.8583080E-03 0.1449223 at 140iterations 4.5261653E-03 8.2277775E-02 at 150iterations 2.6075821E-03 4.9356461E-02 at 160iterations 1.5060916E-03 2.7969360E-02 at 170iterations 8.7048492E-04 1.5987396E-02 at 180iterations finished qdiffx linear iterations at : 20:44:16 total time elapsed so far: 19.35000 # loops : 180 mean,max change (kT/e) : 8.7048492E-04 1.5987396E-02 energy calculations done at 19.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.57000 DelPhi exited at 20:44:16 19.573u 0.525s 0:20.39 98.5% 0+0k 0+0io 0pf+0w