Tue Oct 11 03:14:40 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 03:14:40 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 = 3690 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: 0.5288333 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): 37.19600 94.56900 ymin,ymax (A): 20.73600 72.84000 zmin,zma (A): -8.743999 58.57400 x,y,z range (A): 57.37300 52.10400 67.31800 scale (grids/A): 0.5288333 object centre (A): 65.88250 46.78800 24.91500 number of atom coordinates read : 3690 total number of charged atoms : 3536 net assigned charge : -6.999975 assigned positive charge : 564.5249 centred at (gu) : 89.33003 89.35166 90.73000 assigned negative charge : -571.5276 centred at (gu) : 89.36059 89.33500 90.76832 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6788 nv = 96 ne = 84 npr = 70864 no. pairs analyzed = 70864 no. exposed pairs = 5237 no. arc points = 38098 no. surface atoms = 1716 nbur = 1974 mkacc time = 0.1900000 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= 269 mr = 3099 m= 0 mr = 9 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3745 ## 502 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2216650E-11 -4.6514340E-10 midg,1,midg; midg,igrid,midg -3.4189687E-10 -1.2299585E-10 1,midg,midg; igrid,midg,midg -9.6738492E-11 -2.9752226E-10 gauss-seidel spectral radius is 0.9816487 estimated iterations to convergence 61 setup time was (sec) 0.6800000 now iterating at: 03:14:42 rms-change max change #iterations 6.8390638E-02 11.59703 at 10iterations 4.1869786E-03 0.6531229 at 20iterations 2.5349922E-04 3.9686203E-02 at 30iterations 1.6306096E-05 2.5749207E-03 at 40iterations 1.5069296E-06 1.9550323E-04 at 50iterations finished qdiffx linear iterations at : 03:14:45 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 1.5069296E-06 1.9550323E-04 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 03:14:46 4.750u 0.387s 0:05.63 91.1% 0+0k 0+0io 6pf+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 03:14:46 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 = 3690 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.586500 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): 37.19600 94.56900 ymin,ymax (A): 20.73600 72.84000 zmin,zma (A): -8.743999 58.57400 x,y,z range (A): 57.37300 52.10400 67.31800 scale (grids/A): 1.586500 object centre (A): 65.88250 46.78800 24.91500 number of atom coordinates read : 3690 total number of charged atoms : 3536 net assigned charge : -6.999975 assigned positive charge : 564.5249 centred at (gu) : 87.98898 88.05346 92.18845 assigned negative charge : -571.5276 centred at (gu) : 88.08162 88.00448 92.30455 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38098 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21855 mr = 47811 m= 2088 mr = 13847 m= 49 mr = 842 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 36807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 26859 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) : 0.5288333 object centre at (A) : 65.88250 46.78800 24.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6917208E-02 -7.6144524E-03 midg,1,midg; midg,igrid,midg -6.5134699E-03 -9.1706123E-03 1,midg,midg; igrid,midg,midg 9.7991070E-03 -8.0818264E-03 gauss-seidel spectral radius is 0.9981803 estimated iterations to convergence 186 setup time was (sec) 0.9800000 now iterating at: 03:14:48 rms-change max change #iterations 3.586352 173.5990 at 10iterations 1.482821 53.52910 at 20iterations 0.6152169 21.53435 at 30iterations 0.2564887 9.102610 at 40iterations 0.1061699 3.992197 at 50iterations 4.4258006E-02 1.565462 at 60iterations 1.8381245E-02 0.6259708 at 70iterations 7.6481872E-03 0.2660656 at 80iterations 3.1845754E-03 0.1115799 at 90iterations 1.3273722E-03 4.5646667E-02 at 100iterations 5.5172725E-04 1.8853188E-02 at 110iterations 2.2995977E-04 7.6560974E-03 at 120iterations finished qdiffx linear iterations at : 03:14:58 total time elapsed so far: 10.98000 # loops : 120 mean,max change (kT/e) : 2.2995977E-04 7.6560974E-03 energy calculations done at 10.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 03:14:58 11.151u 0.433s 0:11.93 97.0% 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 03:14:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.379750 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): 37.19600 94.56900 ymin,ymax (A): 20.73600 72.84000 zmin,zma (A): -8.743999 58.57400 x,y,z range (A): 57.37300 52.10400 67.31800 scale (grids/A): 2.379750 object centre (A): 65.88250 46.78800 24.91500 number of atom coordinates read : 3690 total number of charged atoms : 3536 net assigned charge : -6.999975 assigned positive charge : 564.5249 centred at (gu) : 86.98321 87.08017 93.28242 assigned negative charge : -571.5276 centred at (gu) : 87.12225 87.00669 93.45668 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38098 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75542 mr = 118635 m= 20862 mr = 56608 m= 3035 mr = 14690 m= 148 mr = 1669 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 83064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 28237 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) : 1.586500 object centre at (A) : 65.88250 46.78800 24.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5860630 8.3892442E-02 midg,1,midg; midg,igrid,midg -0.1012310 -0.1360057 1,midg,midg; igrid,midg,midg 0.1925626 -0.1037568 gauss-seidel spectral radius is 0.9991775 estimated iterations to convergence 275 setup time was (sec) 1.870000 now iterating at: 03:15:01 rms-change max change #iterations 9.763378 382.2996 at 10iterations 5.642149 154.0806 at 20iterations 3.236067 98.92551 at 30iterations 1.842452 50.25582 at 40iterations 1.047364 22.87836 at 50iterations 0.5903899 13.38824 at 60iterations 0.3323715 7.923134 at 70iterations 0.1872127 3.919404 at 80iterations 0.1049630 2.307506 at 90iterations 5.8902975E-02 1.213558 at 100iterations 3.2896329E-02 0.6695709 at 110iterations 1.8417435E-02 0.4087396 at 120iterations 1.0284799E-02 0.2324524 at 130iterations 5.7513793E-03 0.1096535 at 140iterations 3.2137458E-03 7.4849129E-02 at 150iterations 1.7895560E-03 3.6590576E-02 at 160iterations 1.0003845E-03 2.0656586E-02 at 170iterations 5.5743498E-04 1.1031151E-02 at 180iterations finished qdiffx linear iterations at : 03:15:17 total time elapsed so far: 18.43000 # loops : 180 mean,max change (kT/e) : 5.5743498E-04 1.1031151E-02 energy calculations done at 18.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.59000 DelPhi exited at 03:15:18 18.594u 0.472s 0:19.66 96.9% 0+0k 0+0io 0pf+0w