Sat Oct 8 17:52:04 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 17:52:04 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3294 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5544308 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): -39.05700 10.24100 ymin,ymax (A): 7.861000 72.07100 zmin,zma (A): 62.01600 109.5910 x,y,z range (A): 49.29800 64.21000 47.57500 scale (grids/A): 0.5544308 object centre (A): -14.40800 39.96600 85.80350 number of atom coordinates read : 3294 total number of charged atoms : 3152 net assigned charge : 1.500003 assigned positive charge : 493.5068 centred at (gu) : 89.67628 89.89613 90.18517 assigned negative charge : -492.0080 centred at (gu) : 89.60880 89.84822 90.18100 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6663 nv = 96 ne = 84 npr = 67182 no. pairs analyzed = 67182 no. exposed pairs = 3917 no. arc points = 26698 no. surface atoms = 1331 nbur = 1963 mkacc time = 0.1900000 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= 261 mr = 3701 m= 0 mr = 10 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2848 ## 355 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6992982E-11 1.8246661E-10 midg,1,midg; midg,igrid,midg -3.6087888E-10 5.9576016E-10 1,midg,midg; igrid,midg,midg -5.9786592E-10 7.4347278E-10 gauss-seidel spectral radius is 0.9832423 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 17:52:05 rms-change max change #iterations 8.2678452E-02 16.99431 at 10iterations 5.7592834E-03 0.8929138 at 20iterations 4.1631493E-04 6.4567566E-02 at 30iterations 3.9317496E-05 6.6318512E-03 at 40iterations 6.5305003E-06 1.2609363E-03 at 50iterations finished qdiffx linear iterations at : 17:52:09 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 6.5305003E-06 1.2609363E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 17:52:10 4.563u 0.420s 0:05.26 94.6% 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 Sat Oct 8 2011 at 17:52:10 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3294 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: 1.663292 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): -39.05700 10.24100 ymin,ymax (A): 7.861000 72.07100 zmin,zma (A): 62.01600 109.5910 x,y,z range (A): 49.29800 64.21000 47.57500 scale (grids/A): 1.663292 object centre (A): -14.40800 39.96600 85.80350 number of atom coordinates read : 3294 total number of charged atoms : 3152 net assigned charge : 1.500003 assigned positive charge : 493.5068 centred at (gu) : 89.02792 89.68768 90.55505 assigned negative charge : -492.0080 centred at (gu) : 88.82588 89.54432 90.54262 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26698 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24439 mr = 52546 m= 2693 mr = 17391 m= 86 mr = 1422 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 820 time to turn everything in is 0.6000000 number of dielectric boundary points 29810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 24267 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) : 0.5544308 object centre at (A) : -14.40800 39.96600 85.80350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9055057E-03 -3.4468931E-03 midg,1,midg; midg,igrid,midg 2.0923886E-02 -3.3952824E-03 1,midg,midg; igrid,midg,midg 2.2901429E-03 1.2261113E-02 gauss-seidel spectral radius is 0.9982770 estimated iterations to convergence 191 setup time was (sec) 0.9400000 now iterating at: 17:52:11 rms-change max change #iterations 3.653567 168.1307 at 10iterations 1.554810 58.41844 at 20iterations 0.6663418 22.89941 at 30iterations 0.2838908 9.009756 at 40iterations 0.1209511 4.056402 at 50iterations 5.1820531E-02 1.686626 at 60iterations 2.2165490E-02 0.6917706 at 70iterations 9.4640618E-03 0.2950515 at 80iterations 4.0482413E-03 0.1348495 at 90iterations 1.7397297E-03 5.7561874E-02 at 100iterations 7.4463163E-04 2.5630951E-02 at 110iterations 3.2036810E-04 1.0129929E-02 at 120iterations finished qdiffx linear iterations at : 17:52:20 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 3.2036810E-04 1.0129929E-02 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.49000 DelPhi exited at 17:52:21 10.493u 0.436s 0:11.25 97.0% 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 Sat Oct 8 2011 at 17:52:21 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3294 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: 2.494939 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): -39.05700 10.24100 ymin,ymax (A): 7.861000 72.07100 zmin,zma (A): 62.01600 109.5910 x,y,z range (A): 49.29800 64.21000 47.57500 scale (grids/A): 2.494939 object centre (A): -14.40800 39.96600 85.80350 number of atom coordinates read : 3294 total number of charged atoms : 3152 net assigned charge : 1.500003 assigned positive charge : 493.5068 centred at (gu) : 88.54169 89.53133 90.83239 assigned negative charge : -492.0080 centred at (gu) : 88.23884 89.31625 90.81378 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 171637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26698 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84051 mr = 127665 m= 24916 mr = 68084 m= 4375 mr = 19213 m= 365 mr = 2994 m= 8 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 2818 time to turn everything in is 1.510000 number of dielectric boundary points 67203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 25190 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) : 1.663292 object centre at (A) : -14.40800 39.96600 85.80350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0373156E-02 -4.0156547E-02 midg,1,midg; midg,igrid,midg 0.4668333 7.4814193E-02 1,midg,midg; igrid,midg,midg 6.4119890E-02 0.1672707 gauss-seidel spectral radius is 0.9991698 estimated iterations to convergence 274 setup time was (sec) 1.830000 now iterating at: 17:52:23 rms-change max change #iterations 9.292476 300.5763 at 10iterations 5.246418 125.5168 at 20iterations 2.954629 63.54613 at 30iterations 1.656083 31.68784 at 40iterations 0.9261995 21.21867 at 50iterations 0.5167073 11.18665 at 60iterations 0.2888503 5.654271 at 70iterations 0.1606833 3.256247 at 80iterations 8.9571193E-02 1.774185 at 90iterations 4.9913410E-02 1.106077 at 100iterations 2.7684122E-02 0.5170593 at 110iterations 1.5398572E-02 0.3082018 at 120iterations 8.5689612E-03 0.1728153 at 130iterations 4.7687171E-03 0.1007061 at 140iterations 2.6495883E-03 6.1504364E-02 at 150iterations 1.4771584E-03 2.7282715E-02 at 160iterations 8.2501234E-04 1.6047478E-02 at 170iterations 4.6131981E-04 9.5672607E-03 at 180iterations finished qdiffx linear iterations at : 17:52:39 total time elapsed so far: 17.72000 # loops : 180 mean,max change (kT/e) : 4.6131981E-04 9.5672607E-03 energy calculations done at 17.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.89000 DelPhi exited at 17:52:40 17.894u 0.493s 0:18.66 98.4% 0+0k 0+0io 0pf+0w