Tue Oct 11 06:16:51 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+sph2.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 = amb2.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 06:16:51 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1929 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7231216 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): 20.11600 64.36900 ymin,ymax (A): -3.492000 33.39000 zmin,zma (A): 23.42200 72.65300 x,y,z range (A): 44.25300 36.88200 49.23100 scale (grids/A): 0.7231216 object centre (A): 42.24250 14.94900 48.03750 number of atom coordinates read : 1929 total number of charged atoms : 1879 net assigned charge : 6.025005 assigned positive charge : 304.4632 centred at (gu) : 89.78963 89.76726 88.43285 assigned negative charge : -298.4382 centred at (gu) : 89.96337 89.81806 88.38236 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 36316 no. pairs analyzed = 36316 no. exposed pairs = 2569 no. arc points = 17365 no. surface atoms = 868 nbur = 1061 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 558 mr = 3992 m= 7 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1553 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7744 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2052293E-08 7.9684803E-08 midg,1,midg; midg,igrid,midg 1.1163775E-07 3.7779827E-08 1,midg,midg; igrid,midg,midg 1.9445045E-07 -4.2212225E-08 gauss-seidel spectral radius is 0.9900190 estimated iterations to convergence 81 setup time was (sec) 0.6000000 now iterating at: 06:16:52 rms-change max change #iterations 0.2144687 35.63475 at 10iterations 2.7427958E-02 4.265396 at 20iterations 3.5955072E-03 0.4613495 at 30iterations 5.2347244E-04 7.0526123E-02 at 40iterations 9.8365766E-05 1.3239861E-02 at 50iterations finished qdiffx linear iterations at : 06:16:56 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 9.8365766E-05 1.3239861E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 06:16:56 4.350u 0.406s 0:05.26 90.3% 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 06:16:56 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1929 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.169365 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): 20.11600 64.36900 ymin,ymax (A): -3.492000 33.39000 zmin,zma (A): 23.42200 72.65300 x,y,z range (A): 44.25300 36.88200 49.23100 scale (grids/A): 2.169365 object centre (A): 42.24250 14.94900 48.03750 number of atom coordinates read : 1929 total number of charged atoms : 1879 net assigned charge : 6.025005 assigned positive charge : 304.4632 centred at (gu) : 89.36879 89.30216 85.29890 assigned negative charge : -298.4382 centred at (gu) : 89.89020 89.45442 85.14716 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17365 grid for indexing accessible points = 1.400000 m= 31703 mr = 52064 m= 6999 mr = 24041 m= 744 mr = 4747 m= 21 mr = 384 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 32871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14935 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) : 0.7231216 object centre at (A) : 42.24250 14.94900 48.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5472055E-03 3.2441944E-02 midg,1,midg; midg,igrid,midg 3.3794224E-02 4.4957744E-03 1,midg,midg; igrid,midg,midg 5.4848816E-02 3.1869218E-02 gauss-seidel spectral radius is 0.9988698 estimated iterations to convergence 235 setup time was (sec) 1.120000 now iterating at: 06:16:58 rms-change max change #iterations 4.688360 226.3433 at 10iterations 2.347350 75.37827 at 20iterations 1.180216 37.60688 at 30iterations 0.5918716 16.75677 at 40iterations 0.2979632 10.08088 at 50iterations 0.1498401 4.568194 at 60iterations 7.5068511E-02 2.578338 at 70iterations 3.7754424E-02 1.232040 at 80iterations 1.8982323E-02 0.5683389 at 90iterations 9.5872255E-03 0.2854843 at 100iterations 4.8156306E-03 0.1482143 at 110iterations 2.4531207E-03 7.1014404E-02 at 120iterations finished qdiffx linear iterations at : 06:17:07 total time elapsed so far: 10.22000 # loops : 120 mean,max change (kT/e) : 2.4531207E-03 7.1014404E-02 energy calculations done at 10.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.42000 DelPhi exited at 06:17:08 10.429u 0.468s 0:11.38 95.6% 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 Tue Oct 11 2011 at 06:17:08 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1929 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.254047 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): 20.11600 64.36900 ymin,ymax (A): -3.492000 33.39000 zmin,zma (A): 23.42200 72.65300 x,y,z range (A): 44.25300 36.88200 49.23100 scale (grids/A): 3.254047 object centre (A): 42.24250 14.94900 48.03750 number of atom coordinates read : 1929 total number of charged atoms : 1879 net assigned charge : 6.025005 assigned positive charge : 304.4632 centred at (gu) : 89.05321 88.95329 82.94823 assigned negative charge : -298.4382 centred at (gu) : 89.83537 89.18156 82.72078 start vw surface at 0.1400000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 171650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17365 grid for indexing accessible points = 1.400000 m= 95926 mr = 125246 m= 42261 mr = 79541 m= 13540 mr = 34849 m= 2933 mr = 10550 m= 392 mr = 2122 m= 11 mr = 231 m= 0 mr = 2 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.470000 number of dielectric boundary points 74172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 15023 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) : 2.169365 object centre at (A) : 42.24250 14.94900 48.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8121723E-02 -3.3347342E-02 midg,1,midg; midg,igrid,midg 0.2730162 1.4499269E-02 1,midg,midg; igrid,midg,midg 0.4357849 0.5046720 gauss-seidel spectral radius is 0.9993174 estimated iterations to convergence 302 setup time was (sec) 2.830000 now iterating at: 06:17:11 rms-change max change #iterations 10.49308 330.6639 at 10iterations 6.306811 145.0462 at 20iterations 3.785485 77.13216 at 30iterations 2.262097 45.12691 at 40iterations 1.347944 24.36268 at 50iterations 0.8000274 15.37663 at 60iterations 0.4751693 9.337768 at 70iterations 0.2813996 5.283748 at 80iterations 0.1663465 3.000162 at 90iterations 9.8388381E-02 1.783150 at 100iterations 5.8160223E-02 1.027948 at 110iterations 3.4504417E-02 0.7462454 at 120iterations 2.0470867E-02 0.3742723 at 130iterations 1.2204225E-02 0.2295351 at 140iterations 7.3626707E-03 0.1374269 at 150iterations 4.5325165E-03 8.4489822E-02 at 160iterations 2.8774305E-03 5.0064087E-02 at 170iterations 1.9164338E-03 3.4681320E-02 at 180iterations finished qdiffx linear iterations at : 06:17:26 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 1.9164338E-03 3.4681320E-02 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.13000 DelPhi exited at 06:17:27 18.131u 0.483s 0:18.95 98.2% 0+0k 0+0io 0pf+0w