Mon Oct 10 14:10:37 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 14:10:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5605152 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): -16.12600 34.56400 ymin,ymax (A): -25.87400 37.63900 zmin,zma (A): -3.847000 56.83500 x,y,z range (A): 50.69000 63.51300 60.68200 scale (grids/A): 0.5605152 object centre (A): 9.219002 5.882500 26.49400 number of atom coordinates read : 3182 total number of charged atoms : 3007 net assigned charge : 9.000011 assigned positive charge : 482.6539 centred at (gu) : 89.50159 90.45793 89.38089 assigned negative charge : -473.6551 centred at (gu) : 89.47412 90.54641 89.29381 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6680 nv = 96 ne = 84 npr = 61200 no. pairs analyzed = 61200 no. exposed pairs = 4397 no. arc points = 31882 no. surface atoms = 1456 nbur = 1726 mkacc time = 0.1700000 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 = 1.568000 m= 321 mr = 3257 m= 0 mr = 20 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3096 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8460 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6307725E-11 1.7473912E-09 midg,1,midg; midg,igrid,midg 1.8306068E-09 -1.0000736E-10 1,midg,midg; igrid,midg,midg 7.3964251E-10 1.1732058E-09 gauss-seidel spectral radius is 0.9836073 estimated iterations to convergence 64 setup time was (sec) 0.6600000 now iterating at: 14:10:38 rms-change max change #iterations 8.5249923E-02 14.64454 at 10iterations 6.0764509E-03 0.9686861 at 20iterations 4.4337357E-04 7.2063804E-02 at 30iterations 3.5385805E-05 5.5150986E-03 at 40iterations 3.7480099E-06 4.6920776E-04 at 50iterations finished qdiffx linear iterations at : 14:10:41 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.7480099E-06 4.6920776E-04 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 14:10:41 4.118u 0.270s 0:04.81 91.0% 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 14:10:41 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.681545 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): -16.12600 34.56400 ymin,ymax (A): -25.87400 37.63900 zmin,zma (A): -3.847000 56.83500 x,y,z range (A): 50.69000 63.51300 60.68200 scale (grids/A): 1.681545 object centre (A): 9.219002 5.882500 26.49400 number of atom coordinates read : 3182 total number of charged atoms : 3007 net assigned charge : 9.000011 assigned positive charge : 482.6539 centred at (gu) : 88.50383 91.37295 88.14194 assigned negative charge : -473.6551 centred at (gu) : 88.42235 91.63860 87.88101 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 73138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31882 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22725 mr = 47723 m= 2528 mr = 15042 m= 91 mr = 1268 m= 0 mr = 10 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.6600000 number of dielectric boundary points 34439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23130 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) : 0.5605152 object centre at (A) : 9.219002 5.882500 26.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3335326E-04 1.9427881E-02 midg,1,midg; midg,igrid,midg 1.9696020E-02 1.5797731E-02 1,midg,midg; igrid,midg,midg 7.4858395E-03 5.1557249E-03 gauss-seidel spectral radius is 0.9983280 estimated iterations to convergence 194 setup time was (sec) 0.9500000 now iterating at: 14:10:43 rms-change max change #iterations 3.681958 157.4610 at 10iterations 1.578250 59.66468 at 20iterations 0.6817217 24.38100 at 30iterations 0.2935639 10.15726 at 40iterations 0.1266318 4.146561 at 50iterations 5.4854456E-02 1.850494 at 60iterations 2.3564348E-02 0.8619213 at 70iterations 1.0179078E-02 0.3379326 at 80iterations 4.3957033E-03 0.1615887 at 90iterations 1.8991914E-03 6.7283630E-02 at 100iterations 8.1892521E-04 3.1443566E-02 at 110iterations 3.5409862E-04 1.1924744E-02 at 120iterations finished qdiffx linear iterations at : 14:10:51 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 3.5409862E-04 1.1924744E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 14:10:52 9.438u 0.321s 0:10.26 95.0% 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 14:10:52 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.522318 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): -16.12600 34.56400 ymin,ymax (A): -25.87400 37.63900 zmin,zma (A): -3.847000 56.83500 x,y,z range (A): 50.69000 63.51300 60.68200 scale (grids/A): 2.522318 object centre (A): 9.219002 5.882500 26.49400 number of atom coordinates read : 3182 total number of charged atoms : 3007 net assigned charge : 9.000011 assigned positive charge : 482.6539 centred at (gu) : 87.75568 92.05913 87.21268 assigned negative charge : -473.6551 centred at (gu) : 87.63350 92.45773 86.82138 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 169539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31882 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77165 mr = 116924 m= 22649 mr = 59730 m= 4002 mr = 16534 m= 323 mr = 2576 m= 11 mr = 153 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 1.630000 number of dielectric boundary points 77773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 24039 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) : 1.681545 object centre at (A) : 9.219002 5.882500 26.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1112694 0.3202335 midg,1,midg; midg,igrid,midg 0.3319377 0.2346229 1,midg,midg; igrid,midg,midg 8.6457752E-02 3.7049480E-02 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.950000 now iterating at: 14:10:54 rms-change max change #iterations 9.590178 367.6008 at 10iterations 5.577131 177.5530 at 20iterations 3.225718 107.5286 at 30iterations 1.855872 66.50856 at 40iterations 1.059709 27.86545 at 50iterations 0.6054512 16.95576 at 60iterations 0.3429079 8.972980 at 70iterations 0.1943127 4.513970 at 80iterations 0.1099932 2.517151 at 90iterations 6.2182561E-02 1.663158 at 100iterations 3.5086013E-02 0.8123798 at 110iterations 1.9750515E-02 0.4126520 at 120iterations 1.1128257E-02 0.2395115 at 130iterations 6.2753079E-03 0.1260605 at 140iterations 3.5349112E-03 7.1019173E-02 at 150iterations 1.9901332E-03 4.6119690E-02 at 160iterations 1.1259993E-03 2.2609234E-02 at 170iterations 6.3827512E-04 1.2263298E-02 at 180iterations finished qdiffx linear iterations at : 14:11:08 total time elapsed so far: 15.70000 # loops : 180 mean,max change (kT/e) : 6.3827512E-04 1.2263298E-02 energy calculations done at 15.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.88000 DelPhi exited at 14:11:09 15.885u 0.307s 0:16.82 96.1% 0+0k 0+0io 0pf+0w