Tue Oct 11 05:16:15 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 Tue Oct 11 2011 at 05:16:15 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 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: 0.6894682 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): 16.83600 63.01900 ymin,ymax (A): -3.558000 33.57200 zmin,zma (A): 20.45200 72.08600 x,y,z range (A): 46.18300 37.13000 51.63400 scale (grids/A): 0.6894682 object centre (A): 39.92750 15.00700 46.26900 number of atom coordinates read : 2272 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 90.99650 89.70422 89.24283 assigned negative charge : -309.5042 centred at (gu) : 91.12831 89.72900 89.18583 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6764 nv = 96 ne = 84 npr = 41579 no. pairs analyzed = 41579 no. exposed pairs = 2594 no. arc points = 17347 no. surface atoms = 880 nbur = 1392 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3873 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1680 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0028974E-08 4.6964196E-08 midg,1,midg; midg,igrid,midg 4.6718185E-08 2.6485855E-08 1,midg,midg; igrid,midg,midg 6.4285814E-08 -9.4715871E-09 gauss-seidel spectral radius is 0.9890391 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 05:16:15 rms-change max change #iterations 0.1784386 25.90225 at 10iterations 2.0702949E-02 2.740396 at 20iterations 2.6647681E-03 0.4028225 at 30iterations 4.3404067E-04 5.5009842E-02 at 40iterations 1.1039459E-04 1.4222622E-02 at 50iterations finished qdiffx linear iterations at : 05:16:18 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.1039459E-04 1.4222622E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 05:16:18 3.069u 0.161s 0:03.88 82.9% 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 Tue Oct 11 2011 at 05:16:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.068405 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): 16.83600 63.01900 ymin,ymax (A): -3.558000 33.57200 zmin,zma (A): 20.45200 72.08600 x,y,z range (A): 46.18300 37.13000 51.63400 scale (grids/A): 2.068405 object centre (A): 39.92750 15.00700 46.26900 number of atom coordinates read : 2272 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 92.98942 89.11250 87.72855 assigned negative charge : -309.5042 centred at (gu) : 93.38510 89.18700 87.55759 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 28604 mr = 51043 m= 5307 mr = 21719 m= 415 mr = 3459 m= 7 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15481 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) : 0.6894682 object centre at (A) : 39.92750 15.00700 46.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7632206E-02 3.9656885E-02 midg,1,midg; midg,igrid,midg 2.1821821E-02 1.0936661E-02 1,midg,midg; igrid,midg,midg 2.6630005E-02 1.4939657E-02 gauss-seidel spectral radius is 0.9987760 estimated iterations to convergence 226 setup time was (sec) 0.8100000 now iterating at: 05:16:19 rms-change max change #iterations 4.354425 181.5373 at 10iterations 2.134637 75.10213 at 20iterations 1.038336 37.81602 at 30iterations 0.5111424 17.17862 at 40iterations 0.2500478 8.102434 at 50iterations 0.1219170 4.116432 at 60iterations 5.9871800E-02 1.927686 at 70iterations 2.9336425E-02 0.9296722 at 80iterations 1.4462614E-02 0.4391518 at 90iterations 7.1692658E-03 0.2310066 at 100iterations 3.5720731E-03 0.1128502 at 110iterations 1.8390388E-03 5.8032990E-02 at 120iterations finished qdiffx linear iterations at : 05:16:26 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.8390388E-03 5.8032990E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 05:16:27 7.663u 0.172s 0:08.11 96.5% 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 Tue Oct 11 2011 at 05:16:27 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 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: 3.102607 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): 16.83600 63.01900 ymin,ymax (A): -3.558000 33.57200 zmin,zma (A): 20.45200 72.08600 x,y,z range (A): 46.18300 37.13000 51.63400 scale (grids/A): 3.102607 object centre (A): 39.92750 15.00700 46.26900 number of atom coordinates read : 2272 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 94.48396 88.66894 86.59275 assigned negative charge : -309.5042 centred at (gu) : 95.07771 88.78049 86.33637 start vw surface at 0.1300000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 165138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 89768 mr = 122743 m= 35835 mr = 74682 m= 10049 mr = 29472 m= 1838 mr = 7810 m= 201 mr = 1326 m= 3 mr = 127 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 66670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 15624 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) : 2.068405 object centre at (A) : 39.92750 15.00700 46.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4266711 0.2925025 midg,1,midg; midg,igrid,midg 0.1958434 8.5789874E-02 1,midg,midg; igrid,midg,midg 0.2357737 0.3827861 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 1.900000 now iterating at: 05:16:29 rms-change max change #iterations 9.823835 395.8966 at 10iterations 5.793921 123.0254 at 20iterations 3.406404 66.54135 at 30iterations 1.998256 54.46903 at 40iterations 1.170929 23.71535 at 50iterations 0.6824130 13.59159 at 60iterations 0.3990639 7.294296 at 70iterations 0.2328248 4.374161 at 80iterations 0.1358609 2.816860 at 90iterations 7.9069525E-02 1.407573 at 100iterations 4.6006594E-02 0.8089600 at 110iterations 2.6892982E-02 0.4773812 at 120iterations 1.5710214E-02 0.2970255 at 130iterations 9.2513300E-03 0.1768036 at 140iterations 5.5008810E-03 0.1040993 at 150iterations 3.3214947E-03 6.1262131E-02 at 160iterations 2.0836522E-03 3.6445618E-02 at 170iterations 1.3726512E-03 2.6596069E-02 at 180iterations finished qdiffx linear iterations at : 05:16:39 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 1.3726512E-03 2.6596069E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 05:16:40 12.118u 0.210s 0:12.92 95.3% 0+0k 0+0io 0pf+0w