Sun Oct 9 08:11:14 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+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 08:11:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3454 !!! WARNING: NAP 1080 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5411156 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): 12.30900 78.09900 ymin,ymax (A): 27.32500 79.70800 zmin,zma (A): 61.74800 117.5210 x,y,z range (A): 65.79000 52.38300 55.77301 scale (grids/A): 0.5411156 object centre (A): 45.20400 53.51650 89.63450 number of atom coordinates read : 3454 total number of charged atoms : 3311 net assigned charge : 9.000023 assigned positive charge : 523.0616 centred at (gu) : 89.57870 90.37894 87.41180 assigned negative charge : -514.0632 centred at (gu) : 89.66834 90.42569 87.43295 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6582 nv = 96 ne = 84 npr = 68993 no. pairs analyzed = 68993 no. exposed pairs = 4244 no. arc points = 30357 no. surface atoms = 1418 nbur = 2036 mkacc time = 0.2000000 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= 255 mr = 3485 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.4100000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3079 ## 415 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1171869E-09 1.7424093E-10 midg,1,midg; midg,igrid,midg 6.8150552E-10 1.6867448E-10 1,midg,midg; igrid,midg,midg 1.1276686E-09 -1.0706437E-10 gauss-seidel spectral radius is 0.9824314 estimated iterations to convergence 62 setup time was (sec) 0.6800000 now iterating at: 08:11:15 rms-change max change #iterations 7.4709684E-02 13.33410 at 10iterations 4.9902508E-03 0.6942024 at 20iterations 3.7020189E-04 5.1924706E-02 at 30iterations 4.5939662E-05 6.4659119E-03 at 40iterations 8.9441155E-06 1.2320280E-03 at 50iterations finished qdiffx linear iterations at : 08:11:18 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 8.9441155E-06 1.2320280E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 08:11:19 4.161u 0.261s 0:04.69 94.2% 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 08:11:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3454 !!! WARNING: NAP 1080 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.623347 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): 12.30900 78.09900 ymin,ymax (A): 27.32500 79.70800 zmin,zma (A): 61.74800 117.5210 x,y,z range (A): 65.79000 52.38300 55.77301 scale (grids/A): 1.623347 object centre (A): 45.20400 53.51650 89.63450 number of atom coordinates read : 3454 total number of charged atoms : 3311 net assigned charge : 9.000023 assigned positive charge : 523.0616 centred at (gu) : 88.73528 91.13599 82.23447 assigned negative charge : -514.0632 centred at (gu) : 89.00454 91.27656 82.29852 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 73243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30357 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21821 mr = 50240 m= 2081 mr = 14933 m= 51 mr = 1030 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1249 time to turn everything in is 0.6400000 number of dielectric boundary points 30993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 25304 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) : 0.5411156 object centre at (A) : 45.20400 53.51650 89.63450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3791813E-02 8.3368691E-03 midg,1,midg; midg,igrid,midg 1.2287618E-02 -3.4825052E-03 1,midg,midg; igrid,midg,midg 2.5357261E-02 2.4887803E-03 gauss-seidel spectral radius is 0.9982101 estimated iterations to convergence 188 setup time was (sec) 0.9300000 now iterating at: 08:11:20 rms-change max change #iterations 3.543454 147.0060 at 10iterations 1.484633 52.56700 at 20iterations 0.6249287 25.35889 at 30iterations 0.2620005 9.312180 at 40iterations 0.1101201 4.275024 at 50iterations 4.6403572E-02 1.690018 at 60iterations 1.9520450E-02 0.6834612 at 70iterations 8.1759086E-03 0.2880821 at 80iterations 3.4533939E-03 0.1147690 at 90iterations 1.4536538E-03 4.9005270E-02 at 100iterations 6.1530934E-04 2.1004915E-02 at 110iterations 2.6232857E-04 9.3688965E-03 at 120iterations finished qdiffx linear iterations at : 08:11:28 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 2.6232857E-04 9.3688965E-03 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 08:11:29 9.340u 0.303s 0:10.06 95.8% 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 08:11:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3454 !!! WARNING: NAP 1080 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.435020 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): 12.30900 78.09900 ymin,ymax (A): 27.32500 79.70800 zmin,zma (A): 61.74800 117.5210 x,y,z range (A): 65.79000 52.38300 55.77301 scale (grids/A): 2.435020 object centre (A): 45.20400 53.51650 89.63450 number of atom coordinates read : 3454 total number of charged atoms : 3311 net assigned charge : 9.000023 assigned positive charge : 523.0616 centred at (gu) : 88.10281 91.70373 78.35138 assigned negative charge : -514.0632 centred at (gu) : 88.50675 91.91475 78.44778 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 170648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30357 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 76814 mr = 123469 m= 20811 mr = 60617 m= 3274 mr = 15503 m= 231 mr = 2182 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4023 time to turn everything in is 1.570000 number of dielectric boundary points 69933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 26445 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) : 1.623347 object centre at (A) : 45.20400 53.51650 89.63450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1993170 0.1228525 midg,1,midg; midg,igrid,midg 0.1813291 -5.3436443E-02 1,midg,midg; igrid,midg,midg 0.4201452 2.5106676E-02 gauss-seidel spectral radius is 0.9991544 estimated iterations to convergence 272 setup time was (sec) 1.890000 now iterating at: 08:11:31 rms-change max change #iterations 9.286070 349.7600 at 10iterations 5.274216 156.7277 at 20iterations 2.976083 77.64424 at 30iterations 1.673434 41.17391 at 40iterations 0.9351822 21.72221 at 50iterations 0.5214670 12.43245 at 60iterations 0.2898966 6.039619 at 70iterations 0.1609155 3.756027 at 80iterations 8.9495815E-02 2.162393 at 90iterations 4.9780462E-02 1.019901 at 100iterations 2.7486265E-02 0.5478115 at 110iterations 1.5252132E-02 0.2899251 at 120iterations 8.4532751E-03 0.1642609 at 130iterations 4.6850224E-03 0.1028410 at 140iterations 2.5920495E-03 5.3596497E-02 at 150iterations 1.4331831E-03 3.0512050E-02 at 160iterations 7.9301518E-04 1.6189575E-02 at 170iterations 4.4006371E-04 8.5468292E-03 at 180iterations finished qdiffx linear iterations at : 08:11:45 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 4.4006371E-04 8.5468292E-03 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 08:11:45 15.494u 0.302s 0:16.22 97.3% 0+0k 0+0io 0pf+0w