Sun Oct 9 08:22:06 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 08:22:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5000913 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): -2.765000 68.42200 ymin,ymax (A): -28.39600 38.98300 zmin,zma (A): 24.50400 92.68100 x,y,z range (A): 71.18700 67.37900 68.17700 scale (grids/A): 0.5000913 object centre (A): 32.82850 5.293499 58.59250 number of atom coordinates read : 5714 total number of charged atoms : 5544 net assigned charge : -7.499940 assigned positive charge : 857.8469 centred at (gu) : 89.48748 91.02879 90.58438 assigned negative charge : -865.3536 centred at (gu) : 89.41509 91.02636 90.63390 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8910 nv = 96 ne = 84 npr = 115422 no. pairs analyzed = 115422 no. exposed pairs = 7077 no. arc points = 48615 no. surface atoms = 2380 nbur = 3334 mkacc time = 0.2500000 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 = 1.736000 m= 313 mr = 4621 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5100000 number of dielectric boundary points 4593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4671 ## 704 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7900897E-11 -1.9113272E-10 midg,1,midg; midg,igrid,midg -5.2978337E-11 -7.8007011E-11 1,midg,midg; igrid,midg,midg -2.4055177E-10 6.7322606E-11 gauss-seidel spectral radius is 0.9796199 estimated iterations to convergence 58 setup time was (sec) 0.7400000 now iterating at: 08:22:07 rms-change max change #iterations 6.7767568E-02 10.02169 at 10iterations 4.4530914E-03 0.7795906 at 20iterations 7.9677429E-04 0.1902809 at 30iterations 2.4747138E-04 5.8055878E-02 at 40iterations 8.0645499E-05 1.8257141E-02 at 50iterations finished qdiffx linear iterations at : 08:22:09 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 8.0645499E-05 1.8257141E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 08:22:10 3.525u 0.154s 0:03.96 92.6% 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 08:22:10 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 = 5714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.500274 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): -2.765000 68.42200 ymin,ymax (A): -28.39600 38.98300 zmin,zma (A): 24.50400 92.68100 x,y,z range (A): 71.18700 67.37900 68.17700 scale (grids/A): 1.500274 object centre (A): 32.82850 5.293499 58.59250 number of atom coordinates read : 5714 total number of charged atoms : 5544 net assigned charge : -7.499940 assigned positive charge : 857.8469 centred at (gu) : 88.46119 93.08516 91.75146 assigned negative charge : -865.3536 centred at (gu) : 88.24490 93.07905 91.90160 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 102098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48615 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28363 mr = 70408 m= 2259 mr = 18431 m= 40 mr = 951 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1059 time to turn everything in is 0.7200000 number of dielectric boundary points 42970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 668 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 41290 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) : 0.5000913 object centre at (A) : 32.82850 5.293499 58.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3439873E-03 -1.1859578E-02 midg,1,midg; midg,igrid,midg -7.1979589E-03 -6.6614770E-03 1,midg,midg; igrid,midg,midg -8.8107027E-03 1.7607819E-02 gauss-seidel spectral radius is 0.9981092 estimated iterations to convergence 183 setup time was (sec) 1.010000 now iterating at: 08:22:11 rms-change max change #iterations 4.026381 148.3443 at 10iterations 1.654475 62.61074 at 20iterations 0.6750639 20.76147 at 30iterations 0.2771766 8.555367 at 40iterations 0.1139618 3.624811 at 50iterations 4.6866488E-02 1.416123 at 60iterations 1.9361416E-02 0.6149560 at 70iterations 8.0700144E-03 0.2516212 at 80iterations 3.4028895E-03 0.1066928 at 90iterations 1.4944342E-03 5.1971436E-02 at 100iterations 6.9680333E-04 2.7108192E-02 at 110iterations 3.6012012E-04 1.7265320E-02 at 120iterations finished qdiffx linear iterations at : 08:22:18 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.6012012E-04 1.7265320E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 08:22:18 7.893u 0.200s 0:08.37 96.6% 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 08:22:18 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 = 5714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.250411 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): -2.765000 68.42200 ymin,ymax (A): -28.39600 38.98300 zmin,zma (A): 24.50400 92.68100 x,y,z range (A): 71.18700 67.37900 68.17700 scale (grids/A): 2.250411 object centre (A): 32.82850 5.293499 58.59250 number of atom coordinates read : 5714 total number of charged atoms : 5544 net assigned charge : -7.499940 assigned positive charge : 857.8469 centred at (gu) : 87.69155 94.62712 92.62709 assigned negative charge : -865.3536 centred at (gu) : 87.36713 94.61835 92.85232 start vw surface at 0.2100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 237790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48615 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 103781 mr = 172867 m= 24531 mr = 80167 m= 3173 mr = 17505 m= 135 mr = 1959 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 3485 time to turn everything in is 1.660000 number of dielectric boundary points 96883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 44195 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) : 1.500274 object centre at (A) : 32.82850 5.293499 58.59250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2132593 -0.2796801 midg,1,midg; midg,igrid,midg -8.9035094E-02 -0.1797106 1,midg,midg; igrid,midg,midg 4.8774343E-02 0.4389262 gauss-seidel spectral radius is 0.9991888 estimated iterations to convergence 277 setup time was (sec) 1.990000 now iterating at: 08:22:20 rms-change max change #iterations 11.12744 299.5690 at 10iterations 6.448689 144.2297 at 20iterations 3.724348 89.38369 at 30iterations 2.132834 50.05706 at 40iterations 1.219771 23.06434 at 50iterations 0.6954938 13.95949 at 60iterations 0.3945023 7.521580 at 70iterations 0.2237221 4.244880 at 80iterations 0.1265531 2.384342 at 90iterations 7.1536221E-02 1.297512 at 100iterations 4.0372841E-02 0.6787548 at 110iterations 2.2731019E-02 0.4234223 at 120iterations 1.2834734E-02 0.2181721 at 130iterations 7.2395587E-03 0.1399707 at 140iterations 4.0881312E-03 7.6520920E-02 at 150iterations 2.3194060E-03 3.8368225E-02 at 160iterations 1.3146676E-03 2.2772670E-02 at 170iterations 7.5476622E-04 1.2533188E-02 at 180iterations finished qdiffx linear iterations at : 08:22:31 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 7.5476622E-04 1.2533188E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 08:22:32 13.250u 0.207s 0:13.74 97.8% 0+0k 0+0io 0pf+0w