Sun Oct 9 07:20:20 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 Sun Oct 9 2011 at 07:20:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 0.5440846 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): -5.007000 42.17200 ymin,ymax (A): 35.84800 87.34200 zmin,zma (A): -3.275000 62.15600 x,y,z range (A): 47.17900 51.49400 65.43100 scale (grids/A): 0.5440846 object centre (A): 18.58250 61.59500 29.44050 number of atom coordinates read : 2498 total number of charged atoms : 2353 net assigned charge : -8.499982 assigned positive charge : 372.2330 centred at (gu) : 90.70029 89.08041 89.40092 assigned negative charge : -380.7334 centred at (gu) : 90.85963 88.71272 89.29075 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4898 nv = 96 ne = 84 npr = 49702 no. pairs analyzed = 49702 no. exposed pairs = 3484 no. arc points = 25097 no. surface atoms = 1170 nbur = 1328 mkacc time = 9.9999994E-02 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 = 1.568000 m= 192 mr = 2288 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2505 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6362 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2126969E-09 9.9732542E-11 midg,1,midg; midg,igrid,midg -3.1414564E-09 1.1084482E-09 1,midg,midg; igrid,midg,midg 3.0736103E-10 -1.5648520E-09 gauss-seidel spectral radius is 0.9825560 estimated iterations to convergence 62 setup time was (sec) 0.5000000 now iterating at: 07:20:21 rms-change max change #iterations 6.2631480E-02 11.34703 at 10iterations 4.0008780E-03 0.7611771 at 20iterations 2.6678373E-04 4.9989700E-02 at 30iterations 1.9819494E-05 3.2882690E-03 at 40iterations 2.1313513E-06 3.2043457E-04 at 50iterations finished qdiffx linear iterations at : 07:20:24 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 2.1313513E-06 3.2043457E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 07:20:24 3.195u 0.160s 0:03.66 91.5% 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 Sun Oct 9 2011 at 07:20:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 1.632254 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): -5.007000 42.17200 ymin,ymax (A): 35.84800 87.34200 zmin,zma (A): -3.275000 62.15600 x,y,z range (A): 47.17900 51.49400 65.43100 scale (grids/A): 1.632254 object centre (A): 18.58250 61.59500 29.44050 number of atom coordinates read : 2498 total number of charged atoms : 2353 net assigned charge : -8.499982 assigned positive charge : 372.2330 centred at (gu) : 92.10043 87.24056 88.20229 assigned negative charge : -380.7334 centred at (gu) : 92.57843 86.13784 87.87190 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 53666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25097 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15695 mr = 33945 m= 1454 mr = 10364 m= 39 mr = 626 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 141 time to turn everything in is 0.4100000 number of dielectric boundary points 25919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18053 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) : 0.5440846 object centre at (A) : 18.58250 61.59500 29.44050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5611380E-02 3.9278003E-03 midg,1,midg; midg,igrid,midg -2.1241017E-02 7.8071766E-03 1,midg,midg; igrid,midg,midg -2.1237722E-03 -1.4127327E-02 gauss-seidel spectral radius is 0.9981343 estimated iterations to convergence 184 setup time was (sec) 0.6800000 now iterating at: 07:20:25 rms-change max change #iterations 3.014486 147.0370 at 10iterations 1.237936 61.92345 at 20iterations 0.5073298 21.15070 at 30iterations 0.2084613 8.652478 at 40iterations 8.5623980E-02 3.237842 at 50iterations 3.5250966E-02 1.341429 at 60iterations 1.4479616E-02 0.5793076 at 70iterations 5.9348019E-03 0.2502956 at 80iterations 2.4516534E-03 0.1019564 at 90iterations 1.0118261E-03 4.4200897E-02 at 100iterations 4.1702724E-04 1.7783165E-02 at 110iterations 1.7166922E-04 7.0495605E-03 at 120iterations finished qdiffx linear iterations at : 07:20:32 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.7166922E-04 7.0495605E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 07:20:33 7.878u 0.234s 0:08.47 95.6% 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 07:20:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 2.448381 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): -5.007000 42.17200 ymin,ymax (A): 35.84800 87.34200 zmin,zma (A): -3.275000 62.15600 x,y,z range (A): 47.17900 51.49400 65.43100 scale (grids/A): 2.448381 object centre (A): 18.58250 61.59500 29.44050 number of atom coordinates read : 2498 total number of charged atoms : 2353 net assigned charge : -8.499982 assigned positive charge : 372.2330 centred at (gu) : 93.15041 85.86073 87.30324 assigned negative charge : -380.7334 centred at (gu) : 93.86749 84.20665 86.80769 start vw surface at 0.1500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 124599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25097 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 55289 mr = 83810 m= 14581 mr = 42582 m= 2025 mr = 10465 m= 144 mr = 1207 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 0.9400000 number of dielectric boundary points 58512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 18809 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) : 1.632254 object centre at (A) : 18.58250 61.59500 29.44050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8973607 4.4163901E-02 midg,1,midg; midg,igrid,midg -0.2844111 0.1074562 1,midg,midg; igrid,midg,midg -3.1689465E-02 -0.1832940 gauss-seidel spectral radius is 0.9991164 estimated iterations to convergence 266 setup time was (sec) 1.250000 now iterating at: 07:20:34 rms-change max change #iterations 7.892941 260.9503 at 10iterations 4.387208 126.3002 at 20iterations 2.449241 64.05052 at 30iterations 1.352808 44.43412 at 40iterations 0.7496510 18.52921 at 50iterations 0.4126168 9.128366 at 60iterations 0.2264916 5.093207 at 70iterations 0.1243041 3.179382 at 80iterations 6.8037979E-02 1.511508 at 90iterations 3.7286442E-02 0.8584728 at 100iterations 2.0419426E-02 0.4742851 at 110iterations 1.1134537E-02 0.2730865 at 120iterations 6.0768188E-03 0.1357574 at 130iterations 3.3261999E-03 7.5103760E-02 at 140iterations 1.8138570E-03 4.5925140E-02 at 150iterations 9.9014281E-04 2.4207115E-02 at 160iterations 5.4038927E-04 1.3322830E-02 at 170iterations 2.9399095E-04 6.6375732E-03 at 180iterations finished qdiffx linear iterations at : 07:20:46 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 2.9399095E-04 6.6375732E-03 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 07:20:46 12.798u 0.300s 0:13.40 97.6% 0+0k 0+0io 0pf+0w