Mon Oct 10 19:31:33 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 19:31:34 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 = 2442 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: 0.6950953 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): -18.37700 31.42400 ymin,ymax (A): -6.869000 40.34900 zmin,zma (A): 35.85100 87.06700 x,y,z range (A): 49.80100 47.21800 51.21600 scale (grids/A): 0.6950953 object centre (A): 6.523500 16.74000 61.45900 number of atom coordinates read : 2442 total number of charged atoms : 2305 net assigned charge : 0.5000070 assigned positive charge : 364.4468 centred at (gu) : 90.40260 91.48510 88.69518 assigned negative charge : -363.9475 centred at (gu) : 90.63579 91.49780 88.65611 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8316 nv = 96 ne = 84 npr = 48009 no. pairs analyzed = 48009 no. exposed pairs = 3317 no. arc points = 23044 no. surface atoms = 1102 nbur = 1340 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 636 mr = 4584 m= 3 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 4252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2023 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6997822E-08 1.6140691E-08 midg,1,midg; midg,igrid,midg 7.1294006E-09 -2.0584197E-09 1,midg,midg; igrid,midg,midg 9.4849348E-08 -1.0807884E-07 gauss-seidel spectral radius is 0.9892627 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 19:31:34 rms-change max change #iterations 0.1967379 28.76240 at 10iterations 2.3726027E-02 3.288311 at 20iterations 3.0259893E-03 0.4496899 at 30iterations 5.0536520E-04 7.4165344E-02 at 40iterations 1.5056061E-04 2.1972656E-02 at 50iterations finished qdiffx linear iterations at : 19:31:37 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.5056061E-04 2.1972656E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 19:31:38 3.079u 0.142s 0:04.01 80.0% 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 Mon Oct 10 2011 at 19:31:38 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 = 2442 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: 2.085286 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): -18.37700 31.42400 ymin,ymax (A): -6.869000 40.34900 zmin,zma (A): 35.85100 87.06700 x,y,z range (A): 49.80100 47.21800 51.21600 scale (grids/A): 2.085286 object centre (A): 6.523500 16.74000 61.45900 number of atom coordinates read : 2442 total number of charged atoms : 2305 net assigned charge : 0.5000070 assigned positive charge : 364.4468 centred at (gu) : 91.20731 94.45464 86.08498 assigned negative charge : -363.9475 centred at (gu) : 91.90731 94.49318 85.96812 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 87174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23044 grid for indexing accessible points = 1.400000 m= 36989 mr = 60026 m= 8303 mr = 27945 m= 818 mr = 5710 m= 12 mr = 416 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 39199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18283 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) : 0.6950953 object centre at (A) : 6.523500 16.74000 61.45900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4955947E-03 2.3400752E-02 midg,1,midg; midg,igrid,midg 4.6115317E-03 -5.6527313E-03 1,midg,midg; igrid,midg,midg 4.4313338E-02 -3.7532583E-02 gauss-seidel spectral radius is 0.9988437 estimated iterations to convergence 233 setup time was (sec) 0.9300000 now iterating at: 19:31:39 rms-change max change #iterations 4.877654 268.6130 at 10iterations 2.416472 79.82474 at 20iterations 1.208395 40.16804 at 30iterations 0.5985456 17.29848 at 40iterations 0.2982968 8.376167 at 50iterations 0.1483233 3.870155 at 60iterations 7.4062176E-02 2.152462 at 70iterations 3.6819637E-02 1.006516 at 80iterations 1.8492548E-02 0.5675011 at 90iterations 9.3201334E-03 0.3280163 at 100iterations 4.7293366E-03 0.1383896 at 110iterations 2.4500908E-03 7.4928284E-02 at 120iterations finished qdiffx linear iterations at : 19:31:47 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 2.4500908E-03 7.4928284E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 19:31:47 9.127u 0.234s 0:09.65 96.8% 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 Mon Oct 10 2011 at 19:31:47 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 = 2442 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: 3.127929 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): -18.37700 31.42400 ymin,ymax (A): -6.869000 40.34900 zmin,zma (A): 35.85100 87.06700 x,y,z range (A): 49.80100 47.21800 51.21600 scale (grids/A): 3.127929 object centre (A): 6.523500 16.74000 61.45900 number of atom coordinates read : 2442 total number of charged atoms : 2305 net assigned charge : 0.5000070 assigned positive charge : 364.4468 centred at (gu) : 91.81097 96.68193 84.12726 assigned negative charge : -363.9475 centred at (gu) : 92.86093 96.73974 83.95213 start vw surface at 0.1500000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 200458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23044 grid for indexing accessible points = 1.400000 m= 111015 mr = 144546 m= 49964 mr = 91674 m= 15965 mr = 41272 m= 3318 mr = 12531 m= 332 mr = 2473 m= 10 mr = 201 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 88363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 18436 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) : 2.085286 object centre at (A) : 6.523500 16.74000 61.45900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2594571 0.5435991 midg,1,midg; midg,igrid,midg -8.6982086E-02 -5.2246217E-02 1,midg,midg; igrid,midg,midg 0.3712591 -0.3401940 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 2.420000 now iterating at: 19:31:50 rms-change max change #iterations 11.18951 362.9976 at 10iterations 6.686136 156.5818 at 20iterations 4.007140 84.66277 at 30iterations 2.377756 42.12415 at 40iterations 1.412455 28.09956 at 50iterations 0.8360732 16.01553 at 60iterations 0.4935414 8.025891 at 70iterations 0.2911843 4.846740 at 80iterations 0.1712262 3.056509 at 90iterations 0.1007052 1.847054 at 100iterations 5.9351135E-02 0.9512606 at 110iterations 3.4899235E-02 0.6189756 at 120iterations 2.0534547E-02 0.3465042 at 130iterations 1.2071577E-02 0.1932278 at 140iterations 7.1047489E-03 0.1293454 at 150iterations 4.2064842E-03 6.8264961E-02 at 160iterations 2.5075905E-03 4.2066574E-02 at 170iterations 1.5087422E-03 2.4538040E-02 at 180iterations finished qdiffx linear iterations at : 19:32:03 total time elapsed so far: 15.64000 # loops : 180 mean,max change (kT/e) : 1.5087422E-03 2.4538040E-02 energy calculations done at 15.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.82000 DelPhi exited at 19:32:04 15.817u 0.242s 0:16.91 94.9% 0+0k 0+0io 0pf+0w