Sat Oct 8 17:22:14 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 Sat Oct 8 2011 at 17:22:14 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3471 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: 0.5565631 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): 165.4820 229.4460 ymin,ymax (A): -25.00200 29.06200 zmin,zma (A): -3.215000 51.02800 x,y,z range (A): 63.96399 54.06400 54.24300 scale (grids/A): 0.5565631 object centre (A): 197.4640 2.030001 23.90650 number of atom coordinates read : 3471 total number of charged atoms : 3324 net assigned charge : -6.999965 assigned positive charge : 521.7672 centred at (gu) : 92.07667 88.59022 88.84686 assigned negative charge : -528.7689 centred at (gu) : 92.07792 88.58581 88.81479 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6990 nv = 96 ne = 84 npr = 69876 no. pairs analyzed = 69876 no. exposed pairs = 4538 no. arc points = 30885 no. surface atoms = 1528 nbur = 1943 mkacc time = 0.1600000 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 = 1.540000 m= 330 mr = 3700 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3112 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3400751E-09 -2.1292761E-10 midg,1,midg; midg,igrid,midg -9.7063590E-10 -4.2629486E-10 1,midg,midg; igrid,midg,midg -3.8760797E-10 -1.0788210E-09 gauss-seidel spectral radius is 0.9833854 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 17:22:14 rms-change max change #iterations 9.0779930E-02 15.07007 at 10iterations 6.4979014E-03 0.9201260 at 20iterations 6.4332859E-04 9.1711044E-02 at 30iterations 1.5301362E-04 2.7643204E-02 at 40iterations 4.8877380E-05 9.1009140E-03 at 50iterations finished qdiffx linear iterations at : 17:22:17 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 4.8877380E-05 9.1009140E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:22:17 3.172u 0.141s 0:03.58 92.4% 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 Sat Oct 8 2011 at 17:22:17 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.669690 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): 165.4820 229.4460 ymin,ymax (A): -25.00200 29.06200 zmin,zma (A): -3.215000 51.02800 x,y,z range (A): 63.96399 54.06400 54.24300 scale (grids/A): 1.669690 object centre (A): 197.4640 2.030001 23.90650 number of atom coordinates read : 3471 total number of charged atoms : 3324 net assigned charge : -6.999965 assigned positive charge : 521.7672 centred at (gu) : 96.22900 85.76984 86.53940 assigned negative charge : -528.7689 centred at (gu) : 96.23327 85.75698 86.44386 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30885 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26588 mr = 53346 m= 3304 mr = 18698 m= 112 mr = 1749 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.5600000 number of dielectric boundary points 33426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25527 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) : 0.5565631 object centre at (A) : 197.4640 2.030001 23.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1690199E-03 -1.5215109E-02 midg,1,midg; midg,igrid,midg -1.4439964E-02 1.6153450E-03 1,midg,midg; igrid,midg,midg 5.0673191E-03 4.1676085E-03 gauss-seidel spectral radius is 0.9983065 estimated iterations to convergence 193 setup time was (sec) 0.8200000 now iterating at: 17:22:18 rms-change max change #iterations 3.863603 187.0986 at 10iterations 1.649711 60.14719 at 20iterations 0.7090672 22.55670 at 30iterations 0.3031702 9.796097 at 40iterations 0.1305073 4.214121 at 50iterations 5.6108687E-02 1.795031 at 60iterations 2.4140315E-02 0.7900848 at 70iterations 1.0449992E-02 0.3509960 at 80iterations 4.5424504E-03 0.1464348 at 90iterations 1.9701752E-03 6.2370300E-02 at 100iterations 8.8815280E-04 2.9945374E-02 at 110iterations 4.2005355E-04 1.4747620E-02 at 120iterations finished qdiffx linear iterations at : 17:22:24 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 4.2005355E-04 1.4747620E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 17:22:25 7.095u 0.155s 0:07.52 96.2% 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 Sat Oct 8 2011 at 17:22:25 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.504534 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): 165.4820 229.4460 ymin,ymax (A): -25.00200 29.06200 zmin,zma (A): -3.215000 51.02800 x,y,z range (A): 63.96399 54.06400 54.24300 scale (grids/A): 2.504534 object centre (A): 197.4640 2.030001 23.90650 number of atom coordinates read : 3471 total number of charged atoms : 3324 net assigned charge : -6.999965 assigned positive charge : 521.7672 centred at (gu) : 99.34328 83.65430 84.80880 assigned negative charge : -528.7689 centred at (gu) : 99.34979 83.63544 84.66577 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 179206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30885 grid for indexing accessible points = 1.400000 m= 88404 mr = 130208 m= 28599 mr = 70531 m= 5393 mr = 22061 m= 459 mr = 3597 m= 10 mr = 238 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 525 time to turn everything in is 1.310000 number of dielectric boundary points 75436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 26559 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) : 1.669690 object centre at (A) : 197.4640 2.030001 23.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4542295E-03 -0.1951128 midg,1,midg; midg,igrid,midg -0.1954747 3.1817619E-02 1,midg,midg; igrid,midg,midg 0.1273663 0.2311636 gauss-seidel spectral radius is 0.9991817 estimated iterations to convergence 276 setup time was (sec) 1.600000 now iterating at: 17:22:27 rms-change max change #iterations 9.865922 361.7468 at 10iterations 5.669179 138.5695 at 20iterations 3.241260 72.99231 at 30iterations 1.838104 39.02908 at 40iterations 1.038632 20.53190 at 50iterations 0.5851285 11.20932 at 60iterations 0.3290376 6.706114 at 70iterations 0.1849745 3.546024 at 80iterations 0.1036457 1.904769 at 90iterations 5.8154564E-02 1.052318 at 100iterations 3.2517202E-02 0.6418924 at 110iterations 1.8234583E-02 0.3281384 at 120iterations 1.0211756E-02 0.1980667 at 130iterations 5.6878417E-03 0.1195660 at 140iterations 3.1928634E-03 5.9883118E-02 at 150iterations 1.7832777E-03 3.2797813E-02 at 160iterations 9.9696859E-04 1.8705368E-02 at 170iterations 5.5784459E-04 1.1222839E-02 at 180iterations finished qdiffx linear iterations at : 17:22:36 total time elapsed so far: 11.23000 # loops : 180 mean,max change (kT/e) : 5.5784459E-04 1.1222839E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 17:22:37 11.409u 0.176s 0:11.87 97.4% 0+0k 0+0io 0pf+0w