Tue Oct 11 07:55:32 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 Tue Oct 11 2011 at 07:55:32 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 = 2312 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: 0.7190467 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): 3.884000 53.39400 ymin,ymax (A): -7.775000 39.53700 zmin,zma (A): -24.26500 19.96600 x,y,z range (A): 49.51000 47.31200 44.23100 scale (grids/A): 0.7190467 object centre (A): 28.63900 15.88100 -2.149500 number of atom coordinates read : 2312 total number of charged atoms : 2176 net assigned charge : 4.000010 assigned positive charge : 344.6144 centred at (gu) : 91.08047 90.50135 90.66976 assigned negative charge : -340.6148 centred at (gu) : 91.14590 90.30112 90.57773 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8148 nv = 96 ne = 84 npr = 47208 no. pairs analyzed = 47208 no. exposed pairs = 2750 no. arc points = 19701 no. surface atoms = 927 nbur = 1385 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4734 m= 4 mr = 100 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 3869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1784 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8073472E-08 1.2182107E-07 midg,1,midg; midg,igrid,midg -8.8939849E-08 1.9863920E-07 1,midg,midg; igrid,midg,midg 7.2385390E-08 -3.4130634E-09 gauss-seidel spectral radius is 0.9899409 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 07:55:33 rms-change max change #iterations 0.2268762 27.88635 at 10iterations 2.8992059E-02 4.224038 at 20iterations 3.7005316E-03 0.4498644 at 30iterations 4.7052256E-04 6.1896324E-02 at 40iterations 6.0662569E-05 7.1563721E-03 at 50iterations finished qdiffx linear iterations at : 07:55:35 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 6.0662569E-05 7.1563721E-03 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 07:55:36 3.073u 0.156s 0:03.89 82.7% 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 Tue Oct 11 2011 at 07:55:36 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 = 2312 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: 2.157140 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): 3.884000 53.39400 ymin,ymax (A): -7.775000 39.53700 zmin,zma (A): -24.26500 19.96600 x,y,z range (A): 49.51000 47.31200 44.23100 scale (grids/A): 2.157140 object centre (A): 28.63900 15.88100 -2.149500 number of atom coordinates read : 2312 total number of charged atoms : 2176 net assigned charge : 4.000010 assigned positive charge : 344.6144 centred at (gu) : 93.24118 91.50359 92.00913 assigned negative charge : -340.6148 centred at (gu) : 93.43761 90.90323 91.73313 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 34467 mr = 61255 m= 6913 mr = 26560 m= 624 mr = 4817 m= 17 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 35458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17305 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) : 0.7190467 object centre at (A) : 28.63900 15.88100 -2.149500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4197163E-02 4.0866133E-02 midg,1,midg; midg,igrid,midg 4.7485423E-03 9.8532252E-02 1,midg,midg; igrid,midg,midg 2.0684797E-02 -4.4490108E-03 gauss-seidel spectral radius is 0.9988900 estimated iterations to convergence 238 setup time was (sec) 0.8800000 now iterating at: 07:55:37 rms-change max change #iterations 5.023906 201.9649 at 10iterations 2.528418 86.59795 at 20iterations 1.280195 40.07417 at 30iterations 0.6468856 17.84489 at 40iterations 0.3269108 10.29044 at 50iterations 0.1656566 4.461933 at 60iterations 8.3455160E-02 2.451247 at 70iterations 4.2281643E-02 1.112602 at 80iterations 2.1321408E-02 0.6003771 at 90iterations 1.0793222E-02 0.3016663 at 100iterations 5.4487763E-03 0.1511575 at 110iterations 2.7521595E-03 7.9245567E-02 at 120iterations finished qdiffx linear iterations at : 07:55:43 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 2.7521595E-03 7.9245567E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 07:55:44 7.007u 0.172s 0:07.56 94.8% 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 Tue Oct 11 2011 at 07:55:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 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: 3.235710 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): 3.884000 53.39400 ymin,ymax (A): -7.775000 39.53700 zmin,zma (A): -24.26500 19.96600 x,y,z range (A): 49.51000 47.31200 44.23100 scale (grids/A): 3.235710 object centre (A): 28.63900 15.88100 -2.149500 number of atom coordinates read : 2312 total number of charged atoms : 2176 net assigned charge : 4.000010 assigned positive charge : 344.6144 centred at (gu) : 94.86163 92.25550 93.01366 assigned negative charge : -340.6148 centred at (gu) : 95.15638 91.35475 92.59967 start vw surface at 0.1500000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 199232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 107112 mr = 147383 m= 44362 mr = 89790 m= 13276 mr = 36941 m= 2704 mr = 10550 m= 271 mr = 2088 m= 16 mr = 181 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 80037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 17400 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) : 2.157140 object centre at (A) : 28.63900 15.88100 -2.149500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3088353 0.3421677 midg,1,midg; midg,igrid,midg 5.7375826E-02 0.8897260 1,midg,midg; igrid,midg,midg 8.6587712E-02 3.0587608E-02 gauss-seidel spectral radius is 0.9993110 estimated iterations to convergence 301 setup time was (sec) 2.210000 now iterating at: 07:55:46 rms-change max change #iterations 10.86927 381.8631 at 10iterations 6.400734 119.1562 at 20iterations 3.768882 63.43776 at 30iterations 2.219821 37.42781 at 40iterations 1.301958 22.53041 at 50iterations 0.7636138 12.42163 at 60iterations 0.4479168 7.423649 at 70iterations 0.2625937 4.018114 at 80iterations 0.1542753 2.414753 at 90iterations 9.0394750E-02 1.436905 at 100iterations 5.3093299E-02 0.8354168 at 110iterations 3.1172847E-02 0.4965973 at 120iterations 1.8323468E-02 0.3494301 at 130iterations 1.0779463E-02 0.1734619 at 140iterations 6.3818218E-03 9.9124908E-02 at 150iterations 3.7768360E-03 6.1121941E-02 at 160iterations 2.2592843E-03 3.6338806E-02 at 170iterations 1.3639479E-03 2.2727966E-02 at 180iterations finished qdiffx linear iterations at : 07:55:55 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 1.3639479E-03 2.2727966E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 07:55:56 11.860u 0.169s 0:12.34 97.4% 0+0k 0+0io 0pf+0w