Mon Oct 10 14:41:27 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 Mon Oct 10 2011 at 14:41:27 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2462 !!! WARNING: SEP 323 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5911952 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): -2.936000 44.05400 ymin,ymax (A): 12.62700 72.84400 zmin,zma (A): 54.70000 106.8060 x,y,z range (A): 46.99000 60.21700 52.10600 scale (grids/A): 0.5911952 object centre (A): 20.55900 42.73550 80.75300 number of atom coordinates read : 2462 total number of charged atoms : 2303 net assigned charge : 0.5250087 assigned positive charge : 361.9172 centred at (gu) : 88.89223 90.35559 89.94385 assigned negative charge : -361.3925 centred at (gu) : 88.79762 90.23167 89.94366 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5745 nv = 96 ne = 84 npr = 48792 no. pairs analyzed = 48792 no. exposed pairs = 3348 no. arc points = 23633 no. surface atoms = 1120 nbur = 1342 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 263 mr = 2857 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2217 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7025 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8660290E-10 1.9124029E-10 midg,1,midg; midg,igrid,midg -2.8028662E-09 3.6214856E-09 1,midg,midg; igrid,midg,midg -2.9556648E-09 2.0084894E-09 gauss-seidel spectral radius is 0.9851913 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 14:41:28 rms-change max change #iterations 9.8455861E-02 19.61961 at 10iterations 7.9029342E-03 1.251923 at 20iterations 6.4575725E-04 0.1073036 at 30iterations 5.2928441E-05 9.1190338E-03 at 40iterations 4.3464038E-06 6.7520142E-04 at 50iterations finished qdiffx linear iterations at : 14:41:32 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 4.3464038E-06 6.7520142E-04 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 14:41:33 4.486u 0.394s 0:05.44 89.5% 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 Mon Oct 10 2011 at 14:41:33 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2462 !!! WARNING: SEP 323 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.773585 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): -2.936000 44.05400 ymin,ymax (A): 12.62700 72.84400 zmin,zma (A): 54.70000 106.8060 x,y,z range (A): 46.99000 60.21700 52.10600 scale (grids/A): 1.773585 object centre (A): 20.55900 42.73550 80.75300 number of atom coordinates read : 2462 total number of charged atoms : 2303 net assigned charge : 0.5250087 assigned positive charge : 361.9172 centred at (gu) : 86.67640 91.06641 89.83147 assigned negative charge : -361.3925 centred at (gu) : 86.39241 90.69482 89.83073 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23633 grid for indexing accessible points = 1.400000 m= 20030 mr = 42209 m= 2269 mr = 13399 m= 117 mr = 1034 m= 0 mr = 20 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 29047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17912 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) : 0.5911952 object centre at (A) : 20.55900 42.73550 80.75300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4468916E-03 3.9095748E-03 midg,1,midg; midg,igrid,midg 3.2586216E-03 -2.4361126E-03 1,midg,midg; igrid,midg,midg -2.1261508E-03 2.9893797E-03 gauss-seidel spectral radius is 0.9984212 estimated iterations to convergence 200 setup time was (sec) 0.8500000 now iterating at: 14:41:34 rms-change max change #iterations 3.571795 171.1499 at 10iterations 1.563015 61.40947 at 20iterations 0.6907589 23.94868 at 30iterations 0.3047208 10.08200 at 40iterations 0.1343817 4.805843 at 50iterations 5.9287053E-02 2.232862 at 60iterations 2.6276169E-02 0.9748158 at 70iterations 1.1602597E-02 0.3919754 at 80iterations 5.1427637E-03 0.1886930 at 90iterations 2.2769594E-03 7.9793930E-02 at 100iterations 1.0023656E-03 3.6758423E-02 at 110iterations 4.4503133E-04 1.5443802E-02 at 120iterations finished qdiffx linear iterations at : 14:41:44 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 4.4503133E-04 1.5443802E-02 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.57000 DelPhi exited at 14:41:44 10.571u 0.456s 0:11.35 97.0% 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 Mon Oct 10 2011 at 14:41:44 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2462 !!! WARNING: SEP 323 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.660378 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): -2.936000 44.05400 ymin,ymax (A): 12.62700 72.84400 zmin,zma (A): 54.70000 106.8060 x,y,z range (A): 46.99000 60.21700 52.10600 scale (grids/A): 2.660378 object centre (A): 20.55900 42.73550 80.75300 number of atom coordinates read : 2462 total number of charged atoms : 2303 net assigned charge : 0.5250087 assigned positive charge : 361.9172 centred at (gu) : 85.01444 91.59942 89.74706 assigned negative charge : -361.3925 centred at (gu) : 84.58858 91.04209 89.74596 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 146601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23633 grid for indexing accessible points = 1.400000 m= 68040 mr = 103178 m= 20214 mr = 53294 m= 3568 mr = 14538 m= 396 mr = 2142 m= 17 mr = 227 m= 0 mr = 4 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 65453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 18419 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) : 1.773585 object centre at (A) : 20.55900 42.73550 80.75300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1592140 8.5845180E-02 midg,1,midg; midg,igrid,midg 0.1579203 -0.2015309 1,midg,midg; igrid,midg,midg 1.0136300E-02 1.4863829E-02 gauss-seidel spectral radius is 0.9992025 estimated iterations to convergence 280 setup time was (sec) 1.690000 now iterating at: 14:41:46 rms-change max change #iterations 8.856024 295.5494 at 10iterations 5.136214 150.2999 at 20iterations 2.945723 92.49182 at 30iterations 1.685576 48.67025 at 40iterations 0.9603574 22.33802 at 50iterations 0.5443287 12.13494 at 60iterations 0.3088236 7.126931 at 70iterations 0.1745041 3.656912 at 80iterations 9.8946638E-02 2.269735 at 90iterations 5.5630986E-02 1.342374 at 100iterations 3.1409074E-02 0.6199646 at 110iterations 1.7712327E-02 0.3714104 at 120iterations 9.9732075E-03 0.1991639 at 130iterations 5.6096609E-03 0.1134615 at 140iterations 3.1593894E-03 6.7611694E-02 at 150iterations 1.7795077E-03 3.5171509E-02 at 160iterations 9.9918968E-04 2.0668030E-02 at 170iterations 5.6319352E-04 1.2406349E-02 at 180iterations finished qdiffx linear iterations at : 14:42:02 total time elapsed so far: 17.53000 # loops : 180 mean,max change (kT/e) : 5.6319352E-04 1.2406349E-02 energy calculations done at 17.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 14:42:03 17.714u 0.462s 0:18.63 97.5% 0+0k 0+0io 0pf+0w