Mon Oct 10 14:04:54 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 Mon Oct 10 2011 at 14:04:54 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 0.5249808 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): -9.593000 47.70300 ymin,ymax (A): -19.04800 36.49000 zmin,zma (A): -25.11700 42.69500 x,y,z range (A): 57.29601 55.53800 67.81200 scale (grids/A): 0.5249808 object centre (A): 19.05500 8.720999 8.789000 number of atom coordinates read : 3210 total number of charged atoms : 3074 net assigned charge : 0.5000082 assigned positive charge : 490.5977 centred at (gu) : 88.53774 88.34283 90.38278 assigned negative charge : -490.0989 centred at (gu) : 88.44931 88.40001 90.28442 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5770 nv = 96 ne = 84 npr = 63438 no. pairs analyzed = 63438 no. exposed pairs = 4250 no. arc points = 30231 no. surface atoms = 1436 nbur = 1774 mkacc time = 0.1100000 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 = 1.624000 m= 254 mr = 2833 m= 0 mr = 11 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3016 ## 431 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7794159E-10 3.6004677E-10 midg,1,midg; midg,igrid,midg 3.0293615E-10 -1.1186860E-10 1,midg,midg; igrid,midg,midg -4.0370013E-10 2.0204596E-10 gauss-seidel spectral radius is 0.9813334 estimated iterations to convergence 60 setup time was (sec) 0.4000000 now iterating at: 14:04:54 rms-change max change #iterations 6.2532775E-02 10.56656 at 10iterations 4.3358901E-03 0.7365723 at 20iterations 6.1146595E-04 0.1082020 at 30iterations 1.4670927E-04 2.5390625E-02 at 40iterations 3.7259491E-05 6.6032410E-03 at 50iterations finished qdiffx linear iterations at : 14:04:57 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.7259491E-05 6.6032410E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:04:58 3.376u 0.174s 0:03.88 91.2% 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 Mon Oct 10 2011 at 14:04:58 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 1.574943 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): -9.593000 47.70300 ymin,ymax (A): -19.04800 36.49000 zmin,zma (A): -25.11700 42.69500 x,y,z range (A): 57.29601 55.53800 67.81200 scale (grids/A): 1.574943 object centre (A): 19.05500 8.720999 8.789000 number of atom coordinates read : 3210 total number of charged atoms : 3074 net assigned charge : 0.5000082 assigned positive charge : 490.5977 centred at (gu) : 85.61241 85.02745 91.14733 assigned negative charge : -490.0989 centred at (gu) : 85.34755 85.19967 90.85284 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30231 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19460 mr = 42060 m= 2105 mr = 12936 m= 50 mr = 972 m= 0 mr = 1 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 139 time to turn everything in is 0.3200000 number of dielectric boundary points 29512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23346 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) : 0.5249808 object centre at (A) : 19.05500 8.720999 8.789000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9683891E-03 3.2321420E-02 midg,1,midg; midg,igrid,midg 9.6387608E-04 -8.5585564E-03 1,midg,midg; igrid,midg,midg -1.0760556E-02 5.9179636E-04 gauss-seidel spectral radius is 0.9980727 estimated iterations to convergence 181 setup time was (sec) 0.5400000 now iterating at: 14:04:58 rms-change max change #iterations 3.225772 167.8440 at 10iterations 1.307746 54.47793 at 20iterations 0.5307136 21.52234 at 30iterations 0.2141074 7.680333 at 40iterations 8.7175287E-02 3.276361 at 50iterations 3.5521716E-02 1.569567 at 60iterations 1.4484907E-02 0.5625639 at 70iterations 5.9700590E-03 0.2442436 at 80iterations 2.5137640E-03 0.1007080 at 90iterations 1.1031677E-03 4.3647766E-02 at 100iterations 5.1441434E-04 2.0437241E-02 at 110iterations 2.6350099E-04 1.1096954E-02 at 120iterations finished qdiffx linear iterations at : 14:05:05 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 2.6350099E-04 1.1096954E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 14:05:06 7.611u 0.188s 0:08.34 93.4% 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 Mon Oct 10 2011 at 14:05:06 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 2.362414 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): -9.593000 47.70300 ymin,ymax (A): -19.04800 36.49000 zmin,zma (A): -25.11700 42.69500 x,y,z range (A): 57.29601 55.53800 67.81200 scale (grids/A): 2.362414 object centre (A): 19.05500 8.720999 8.789000 number of atom coordinates read : 3210 total number of charged atoms : 3074 net assigned charge : 0.5000082 assigned positive charge : 490.5977 centred at (gu) : 83.41852 82.54094 91.72073 assigned negative charge : -490.0989 centred at (gu) : 83.02119 82.79940 91.27912 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 147961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30231 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 67176 mr = 103044 m= 19348 mr = 51978 m= 3257 mr = 13938 m= 208 mr = 2082 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 541 time to turn everything in is 0.7900000 number of dielectric boundary points 66847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24544 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) : 1.574943 object centre at (A) : 19.05500 8.720999 8.789000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0977036E-02 0.5847404 midg,1,midg; midg,igrid,midg 1.5418159E-02 -0.1511963 1,midg,midg; igrid,midg,midg -0.1654311 -2.7366916E-03 gauss-seidel spectral radius is 0.9991060 estimated iterations to convergence 264 setup time was (sec) 1.020000 now iterating at: 14:05:07 rms-change max change #iterations 8.701838 279.4503 at 10iterations 4.880869 150.0389 at 20iterations 2.711076 73.33527 at 30iterations 1.498608 34.39278 at 40iterations 0.8240101 20.23270 at 50iterations 0.4516248 10.79063 at 60iterations 0.2469781 5.207491 at 70iterations 0.1351890 3.101625 at 80iterations 7.3695049E-02 1.653671 at 90iterations 4.0131446E-02 0.8428733 at 100iterations 2.1859419E-02 0.4556732 at 110iterations 1.1915809E-02 0.2630630 at 120iterations 6.4995298E-03 0.1425357 at 130iterations 3.5535081E-03 7.9292297E-02 at 140iterations 1.9472804E-03 4.5780182E-02 at 150iterations 1.0763468E-03 2.2895813E-02 at 160iterations 6.0233020E-04 1.2729645E-02 at 170iterations 3.4447244E-04 8.1176758E-03 at 180iterations finished qdiffx linear iterations at : 14:05:18 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 3.4447244E-04 8.1176758E-03 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 14:05:19 12.168u 0.189s 0:12.78 96.5% 0+0k 0+0io 0pf+0w