Sun Oct 9 11:11:32 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 11:11:32 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 = 2880 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: 0.5846993 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): -20.50700 40.37900 ymin,ymax (A): -29.52700 29.27500 zmin,zma (A): 1.153000 55.84600 x,y,z range (A): 60.88600 58.80200 54.69300 scale (grids/A): 0.5846993 object centre (A): 9.935999 -0.1260004 28.49950 number of atom coordinates read : 2880 total number of charged atoms : 2809 net assigned charge : 6.500018 assigned positive charge : 433.1050 centred at (gu) : 90.54314 91.15431 88.95722 assigned negative charge : -426.6068 centred at (gu) : 90.54122 91.16551 89.03668 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6792 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 4123 no. arc points = 28888 no. surface atoms = 1361 nbur = 1519 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 = 1.484000 m= 377 mr = 3346 m= 2 mr = 34 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 0.2000000 number of dielectric boundary points 3791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2910 ## 318 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5671036E-09 -2.3921251E-10 midg,1,midg; midg,igrid,midg 1.4823750E-09 1.7752692E-09 1,midg,midg; igrid,midg,midg 1.4164665E-09 1.9151687E-09 gauss-seidel spectral radius is 0.9849083 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 11:11:33 rms-change max change #iterations 9.7327098E-02 16.91951 at 10iterations 7.7169021E-03 1.182486 at 20iterations 6.9700467E-04 9.4659805E-02 at 30iterations 9.7601012E-05 1.4545441E-02 at 40iterations 2.1321486E-05 2.5959015E-03 at 50iterations finished qdiffx linear iterations at : 11:11:36 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.1321486E-05 2.5959015E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 11:11:36 3.488u 0.170s 0:03.99 91.4% 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 11:11:36 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 = 2880 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: 1.754098 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): -20.50700 40.37900 ymin,ymax (A): -29.52700 29.27500 zmin,zma (A): 1.153000 55.84600 x,y,z range (A): 60.88600 58.80200 54.69300 scale (grids/A): 1.754098 object centre (A): 9.935999 -0.1260004 28.49950 number of atom coordinates read : 2880 total number of charged atoms : 2809 net assigned charge : 6.500018 assigned positive charge : 433.1050 centred at (gu) : 91.62845 93.46222 86.87080 assigned negative charge : -426.6068 centred at (gu) : 91.62335 93.49649 87.10985 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28888 grid for indexing accessible points = 1.400000 m= 24240 mr = 48885 m= 3397 mr = 16393 m= 143 mr = 1819 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 162 time to turn everything in is 0.3700000 number of dielectric boundary points 34906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21909 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) : 0.5846993 object centre at (A) : 9.935999 -0.1260004 28.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1615008E-02 -4.9111973E-03 midg,1,midg; midg,igrid,midg 2.2837346E-02 3.2488156E-02 1,midg,midg; igrid,midg,midg -6.4163357E-03 1.5435529E-02 gauss-seidel spectral radius is 0.9984514 estimated iterations to convergence 202 setup time was (sec) 0.5900000 now iterating at: 11:11:37 rms-change max change #iterations 3.797962 182.8065 at 10iterations 1.678807 66.89293 at 20iterations 0.7465309 25.77371 at 30iterations 0.3338203 11.22689 at 40iterations 0.1480931 5.276768 at 50iterations 6.5889589E-02 2.093987 at 60iterations 2.9296434E-02 0.9400865 at 70iterations 1.3068590E-02 0.4228134 at 80iterations 5.8419313E-03 0.2018738 at 90iterations 2.6103831E-03 9.8592758E-02 at 100iterations 1.1720614E-03 3.9369583E-02 at 110iterations 5.2859436E-04 1.8002510E-02 at 120iterations finished qdiffx linear iterations at : 11:11:44 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 5.2859436E-04 1.8002510E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 11:11:45 7.915u 0.196s 0:08.55 94.7% 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 11:11:45 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 = 2880 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: 2.631147 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): -20.50700 40.37900 ymin,ymax (A): -29.52700 29.27500 zmin,zma (A): 1.153000 55.84600 x,y,z range (A): 60.88600 58.80200 54.69300 scale (grids/A): 2.631147 object centre (A): 9.935999 -0.1260004 28.49950 number of atom coordinates read : 2880 total number of charged atoms : 2809 net assigned charge : 6.500018 assigned positive charge : 433.1050 centred at (gu) : 92.44253 95.19321 85.30596 assigned negative charge : -426.6068 centred at (gu) : 92.43500 95.24477 85.66470 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28888 grid for indexing accessible points = 1.400000 m= 80264 mr = 120102 m= 26437 mr = 62064 m= 5726 mr = 19856 m= 605 mr = 3899 m= 17 mr = 302 m= 0 mr = 4 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 495 time to turn everything in is 0.9300000 number of dielectric boundary points 78835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22462 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) : 1.754098 object centre at (A) : 9.935999 -0.1260004 28.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1542983 -4.7363725E-02 midg,1,midg; midg,igrid,midg 0.2791685 0.4697344 1,midg,midg; igrid,midg,midg -0.1436811 0.3225426 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.160000 now iterating at: 11:11:46 rms-change max change #iterations 9.597013 257.2679 at 10iterations 5.677135 144.2650 at 20iterations 3.313400 88.86790 at 30iterations 1.916906 38.28366 at 40iterations 1.106398 23.73783 at 50iterations 0.6362637 13.50226 at 60iterations 0.3652157 7.431739 at 70iterations 0.2086307 3.970468 at 80iterations 0.1192911 2.348831 at 90iterations 6.8042673E-02 1.329843 at 100iterations 3.8779825E-02 0.8573380 at 110iterations 2.2042876E-02 0.4484806 at 120iterations 1.2572110E-02 0.2315805 at 130iterations 7.1475860E-03 0.1336193 at 140iterations 4.0805186E-03 7.9296112E-02 at 150iterations 2.3178523E-03 4.3111801E-02 at 160iterations 1.3208528E-03 2.7065277E-02 at 170iterations 7.5113459E-04 1.5048981E-02 at 180iterations finished qdiffx linear iterations at : 11:11:58 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 7.5113459E-04 1.5048981E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 11:11:58 12.692u 0.210s 0:13.27 97.2% 0+0k 0+0io 0pf+0w