Sun Oct 9 08:36:54 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 Sun Oct 9 2011 at 08:36:54 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6140 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4767836 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): -15.07900 51.91400 ymin,ymax (A): -16.61100 49.62400 zmin,zma (A): -6.363000 68.30400 x,y,z range (A): 66.99300 66.23500 74.66700 scale (grids/A): 0.4767836 object centre (A): 18.41750 16.50650 30.97050 number of atom coordinates read : 6140 total number of charged atoms : 5971 net assigned charge : -3.985987 assigned positive charge : 926.6934 centred at (gu) : 89.87813 90.45597 90.67763 assigned negative charge : -930.6876 centred at (gu) : 89.94929 90.39763 90.75685 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8648 nv = 96 ne = 84 npr = 122940 no. pairs analyzed = 122940 no. exposed pairs = 7714 no. arc points = 53676 no. surface atoms = 2560 nbur = 3580 mkacc time = 0.2100000 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 = 1.792000 m= 282 mr = 4352 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4000000 number of dielectric boundary points 4575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5015 ## 896 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11807 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7259047E-11 -8.3293983E-11 midg,1,midg; midg,igrid,midg -4.6944459E-11 3.4837945E-11 1,midg,midg; igrid,midg,midg 4.0983203E-11 -6.0644240E-11 gauss-seidel spectral radius is 0.9776166 estimated iterations to convergence 55 setup time was (sec) 0.5900000 now iterating at: 08:36:55 rms-change max change #iterations 5.4993518E-02 9.538467 at 10iterations 2.9707130E-03 0.5136509 at 20iterations 4.5341565E-04 0.1169052 at 30iterations 1.3035891E-04 3.2920837E-02 at 40iterations 4.0551880E-05 9.7885132E-03 at 50iterations finished qdiffx linear iterations at : 08:36:58 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 4.0551880E-05 9.7885132E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 08:36:58 3.640u 0.183s 0:04.09 93.3% 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 Sun Oct 9 2011 at 08:36:58 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6140 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.430351 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): -15.07900 51.91400 ymin,ymax (A): -16.61100 49.62400 zmin,zma (A): -6.363000 68.30400 x,y,z range (A): 66.99300 66.23500 74.66700 scale (grids/A): 1.430351 object centre (A): 18.41750 16.50650 30.97050 number of atom coordinates read : 6140 total number of charged atoms : 5971 net assigned charge : -3.985987 assigned positive charge : 926.6934 centred at (gu) : 89.63224 91.36571 92.03127 assigned negative charge : -930.6876 centred at (gu) : 89.84756 91.19260 92.27010 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 99964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53676 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 26140 mr = 68043 m= 1754 mr = 16432 m= 22 mr = 544 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 0.5000000 number of dielectric boundary points 42861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 866 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 43693 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) : 0.4767836 object centre at (A) : 18.41750 16.50650 30.97050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7678651E-03 -3.1550735E-02 midg,1,midg; midg,igrid,midg -8.7212939E-03 2.5499135E-03 1,midg,midg; igrid,midg,midg 1.2357967E-02 -3.5007403E-04 gauss-seidel spectral radius is 0.9979278 estimated iterations to convergence 175 setup time was (sec) 0.7200000 now iterating at: 08:36:59 rms-change max change #iterations 3.738781 138.0596 at 10iterations 1.468076 47.88184 at 20iterations 0.5763162 18.19092 at 30iterations 0.2271554 7.650299 at 40iterations 8.9598350E-02 2.925735 at 50iterations 3.5306785E-02 1.160595 at 60iterations 1.3980421E-02 0.3964105 at 70iterations 5.5738729E-03 0.1892509 at 80iterations 2.2632929E-03 8.2867622E-02 at 90iterations 9.5729047E-04 3.5464048E-02 at 100iterations 4.3812217E-04 1.9332886E-02 at 110iterations 2.2754449E-04 9.8876953E-03 at 120iterations finished qdiffx linear iterations at : 08:37:06 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.2754449E-04 9.8876953E-03 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 08:37:07 7.968u 0.197s 0:08.48 96.1% 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 08:37:07 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6140 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.145526 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): -15.07900 51.91400 ymin,ymax (A): -16.61100 49.62400 zmin,zma (A): -6.363000 68.30400 x,y,z range (A): 66.99300 66.23500 74.66700 scale (grids/A): 2.145526 object centre (A): 18.41750 16.50650 30.97050 number of atom coordinates read : 6140 total number of charged atoms : 5971 net assigned charge : -3.985987 assigned positive charge : 926.6934 centred at (gu) : 89.44791 92.04813 93.04662 assigned negative charge : -930.6876 centred at (gu) : 89.77112 91.78878 93.40500 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 233794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53676 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 98464 mr = 168438 m= 20928 mr = 74969 m= 2193 mr = 14104 m= 63 mr = 1096 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 772 time to turn everything in is 1.170000 number of dielectric boundary points 96836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 47489 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) : 1.430351 object centre at (A) : 18.41750 16.50650 30.97050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1999085 -0.8895314 midg,1,midg; midg,igrid,midg -0.1800021 9.2865661E-02 1,midg,midg; igrid,midg,midg 0.3113201 1.6974732E-02 gauss-seidel spectral radius is 0.9991414 estimated iterations to convergence 270 setup time was (sec) 1.420000 now iterating at: 08:37:08 rms-change max change #iterations 10.71715 283.1410 at 10iterations 6.144651 133.6118 at 20iterations 3.500099 71.43280 at 30iterations 1.977574 50.74856 at 40iterations 1.116142 23.17634 at 50iterations 0.6267775 12.35847 at 60iterations 0.3510231 6.850136 at 70iterations 0.1960778 3.643303 at 80iterations 0.1094249 2.420403 at 90iterations 6.0792711E-02 1.136922 at 100iterations 3.3932440E-02 0.6939025 at 110iterations 1.8821981E-02 0.3695698 at 120iterations 1.0457396E-02 0.1913847 at 130iterations 5.7923789E-03 0.1266568 at 140iterations 3.2233030E-03 6.1554193E-02 at 150iterations 1.7933935E-03 3.6813021E-02 at 160iterations 1.0003251E-03 2.4479866E-02 at 170iterations 5.6205021E-04 1.1034012E-02 at 180iterations finished qdiffx linear iterations at : 08:37:20 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 5.6205021E-04 1.1034012E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 08:37:21 13.455u 0.209s 0:13.94 97.9% 0+0k 0+0io 0pf+0w