Sun Oct 9 13:48:14 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 Sun Oct 9 2011 at 13:48:14 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.7116868 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): -1.181000 45.48700 ymin,ymax (A): 36.39100 86.41300 zmin,zma (A): -24.52200 24.79700 x,y,z range (A): 46.66800 50.02200 49.31900 scale (grids/A): 0.7116868 object centre (A): 22.15300 61.40200 0.1374998 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.8292 centred at (gu) : 89.97424 89.92221 91.68113 assigned negative charge : -359.4236 centred at (gu) : 90.10419 90.02610 91.62116 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8241 nv = 96 ne = 84 npr = 47391 no. pairs analyzed = 47391 no. exposed pairs = 2978 no. arc points = 20870 no. surface atoms = 999 nbur = 1367 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4632 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 4044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1844 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8935 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3446184E-09 9.4705626E-08 midg,1,midg; midg,igrid,midg 9.6647753E-08 -3.3996798E-08 1,midg,midg; igrid,midg,midg 1.1165051E-07 -5.0936862E-08 gauss-seidel spectral radius is 0.9897397 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 13:48:15 rms-change max change #iterations 0.2282112 28.21072 at 10iterations 2.9061520E-02 3.561317 at 20iterations 4.2681275E-03 0.5679436 at 30iterations 9.5789123E-04 0.1588097 at 40iterations 3.1102711E-04 5.1223755E-02 at 50iterations finished qdiffx linear iterations at : 13:48:17 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.1102711E-04 5.1223755E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 13:48:18 3.307u 0.186s 0:03.77 92.3% 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 Sun Oct 9 2011 at 13:48:18 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.135061 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): -1.181000 45.48700 ymin,ymax (A): 36.39100 86.41300 zmin,zma (A): -24.52200 24.79700 x,y,z range (A): 46.66800 50.02200 49.31900 scale (grids/A): 2.135061 object centre (A): 22.15300 61.40200 0.1374998 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.8292 centred at (gu) : 89.92241 89.76644 95.04308 assigned negative charge : -359.4236 centred at (gu) : 90.31239 90.07803 94.86335 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20870 grid for indexing accessible points = 1.400000 m= 33860 mr = 60613 m= 6244 mr = 25345 m= 558 mr = 3996 m= 15 mr = 273 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 37257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17643 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) : 0.7116868 object centre at (A) : 22.15300 61.40200 0.1374998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7385926E-02 2.9954245E-02 midg,1,midg; midg,igrid,midg 0.1065469 -1.5735059E-03 1,midg,midg; igrid,midg,midg -7.6533649E-03 -1.7490763E-02 gauss-seidel spectral radius is 0.9988802 estimated iterations to convergence 236 setup time was (sec) 0.6400000 now iterating at: 13:48:19 rms-change max change #iterations 5.088957 205.3791 at 10iterations 2.551258 97.90673 at 20iterations 1.276553 37.04073 at 30iterations 0.6455270 23.72562 at 40iterations 0.3242868 9.936179 at 50iterations 0.1636782 4.877339 at 60iterations 8.2435749E-02 2.381177 at 70iterations 4.1802276E-02 1.335655 at 80iterations 2.1207340E-02 0.5807686 at 90iterations 1.0930894E-02 0.3204346 at 100iterations 5.6637288E-03 0.1690731 at 110iterations 3.0291129E-03 9.6099854E-02 at 120iterations finished qdiffx linear iterations at : 13:48:26 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.0291129E-03 9.6099854E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 13:48:26 7.787u 0.202s 0:08.26 96.6% 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 Sun Oct 9 2011 at 13:48:26 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.202591 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): -1.181000 45.48700 ymin,ymax (A): 36.39100 86.41300 zmin,zma (A): -24.52200 24.79700 x,y,z range (A): 46.66800 50.02200 49.31900 scale (grids/A): 3.202591 object centre (A): 22.15300 61.40200 0.1374998 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.8292 centred at (gu) : 89.88343 89.64957 97.56448 assigned negative charge : -359.4236 centred at (gu) : 90.46847 90.11690 97.29498 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 199770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20870 grid for indexing accessible points = 1.400000 m= 106239 mr = 145851 m= 42204 mr = 87807 m= 11606 mr = 34176 m= 2317 mr = 8831 m= 278 mr = 1659 m= 10 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 83923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 17768 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) : 2.135061 object centre at (A) : 22.15300 61.40200 0.1374998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3271423 0.4360369 midg,1,midg; midg,igrid,midg 1.456334 -0.1561252 1,midg,midg; igrid,midg,midg -0.1328789 -0.1412314 gauss-seidel spectral radius is 0.9993138 estimated iterations to convergence 301 setup time was (sec) 1.550000 now iterating at: 13:48:28 rms-change max change #iterations 11.37173 387.7195 at 10iterations 6.799805 156.3835 at 20iterations 4.055532 86.10669 at 30iterations 2.414114 44.55095 at 40iterations 1.431403 26.48278 at 50iterations 0.8476992 16.54594 at 60iterations 0.5009795 8.615950 at 70iterations 0.2971380 4.930756 at 80iterations 0.1750152 3.048311 at 90iterations 0.1035134 1.830065 at 100iterations 6.1261818E-02 1.083827 at 110iterations 3.6454719E-02 0.6233711 at 120iterations 2.1864006E-02 0.4074860 at 130iterations 1.3375674E-02 0.2319908 at 140iterations 8.4269391E-03 0.1587830 at 150iterations 5.5825370E-03 0.1259689 at 160iterations 3.9222096E-03 8.5334778E-02 at 170iterations 2.9402925E-03 6.3987732E-02 at 180iterations finished qdiffx linear iterations at : 13:48:39 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 2.9402925E-03 6.3987732E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 13:48:40 13.050u 0.214s 0:13.54 97.9% 0+0k 0+0io 0pf+0w