Wed Feb 15 08:54:44 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 0.5626502 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 0.5626502 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999973 assigned positive charge : 540.9236 centred at (gu) : 88.89059 86.26514 91.02016 assigned negative charge : -544.9257 centred at (gu) : 88.94273 86.20561 90.96233 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7461 nv = 96 ne = 84 npr = 72778 no. pairs analyzed = 72778 no. exposed pairs = 4716 no. arc points = 33002 no. surface atoms = 1582 nbur = 2026 mkacc time = 0.1200000 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 = 1.512000 m= 325 mr = 3847 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3396 ## 417 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0124014E-09 5.1658833E-10 midg,1,midg; midg,igrid,midg -3.3088825E-09 1.6406437E-10 1,midg,midg; igrid,midg,midg 4.2116721E-10 -9.2697083E-10 gauss-seidel spectral radius is 0.9837555 estimated iterations to convergence 65 setup time was (sec) 0.4500000 now iterating at: 08:54:45 rms-change max change #iterations 9.3139306E-02 15.42287 at 10iterations 6.7447405E-03 1.013420 at 20iterations 5.5433298E-04 8.7860107E-02 at 30iterations 7.7335659E-05 1.5726566E-02 at 40iterations 1.8341439E-05 4.1139126E-03 at 50iterations finished qdiffx linear iterations at : 08:54:48 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.8341439E-05 4.1139126E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:54:49 3.537u 0.179s 0:04.51 82.0% 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 Wed Feb 15 2012 at 08:54:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 1.687951 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 1.687951 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999973 assigned positive charge : 540.9236 centred at (gu) : 86.67062 78.79427 93.05933 assigned negative charge : -544.9257 centred at (gu) : 86.82781 78.61627 92.88641 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33002 grid for indexing accessible points = 1.400000 m= 26781 mr = 56036 m= 3074 mr = 18246 m= 94 mr = 1523 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.4000000 number of dielectric boundary points 36475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 26747 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) : 0.5626502 object centre at (A) : 29.04900 13.32100 24.87950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2301050E-04 5.0927787E-03 midg,1,midg; midg,igrid,midg -3.6390591E-02 2.2555836E-03 1,midg,midg; igrid,midg,midg -1.3288442E-02 -3.4821458E-02 gauss-seidel spectral radius is 0.9983587 estimated iterations to convergence 196 setup time was (sec) 0.6200000 now iterating at: 08:54:51 rms-change max change #iterations 3.955453 184.1738 at 10iterations 1.713531 65.62959 at 20iterations 0.7501690 24.25726 at 30iterations 0.3251072 11.55936 at 40iterations 0.1416427 4.537429 at 50iterations 6.1735678E-02 1.886358 at 60iterations 2.6902774E-02 0.9628024 at 70iterations 1.1702989E-02 0.3682714 at 80iterations 5.0885323E-03 0.1795883 at 90iterations 2.2334920E-03 7.1727753E-02 at 100iterations 9.7593811E-04 3.3187866E-02 at 110iterations 4.3028142E-04 1.2830734E-02 at 120iterations finished qdiffx linear iterations at : 08:54:59 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 4.3028142E-04 1.2830734E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 08:54:59 7.981u 0.206s 0:10.58 77.3% 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 Wed Feb 15 2012 at 08:54:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 2.531926 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 2.531926 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999973 assigned positive charge : 540.9236 centred at (gu) : 85.00583 73.19131 94.58884 assigned negative charge : -544.9257 centred at (gu) : 85.24160 72.92420 94.32955 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 191032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33002 grid for indexing accessible points = 1.400000 m= 90986 mr = 136836 m= 27175 mr = 71788 m= 4905 mr = 20287 m= 359 mr = 3116 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 1.100000 number of dielectric boundary points 82315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 27660 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) : 1.687951 object centre at (A) : 29.04900 13.32100 24.87950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2260601E-02 0.2611426 midg,1,midg; midg,igrid,midg -0.5181231 1.9563055E-02 1,midg,midg; igrid,midg,midg -0.1933803 -0.6515622 gauss-seidel spectral radius is 0.9992065 estimated iterations to convergence 280 setup time was (sec) 1.390000 now iterating at: 08:55:01 rms-change max change #iterations 10.18919 329.8077 at 10iterations 5.895755 154.0666 at 20iterations 3.380433 84.70505 at 30iterations 1.929417 41.70546 at 40iterations 1.095021 21.14636 at 50iterations 0.6230041 12.23921 at 60iterations 0.3528762 6.803172 at 70iterations 0.1997056 3.855906 at 80iterations 0.1126559 2.298103 at 90iterations 6.3682094E-02 1.207824 at 100iterations 3.5920948E-02 0.6383877 at 110iterations 2.0267956E-02 0.4421577 at 120iterations 1.1439644E-02 0.2046661 at 130iterations 6.4632460E-03 0.1380343 at 140iterations 3.6303648E-03 6.5384865E-02 at 150iterations 2.0537237E-03 3.6857605E-02 at 160iterations 1.1608242E-03 2.1835327E-02 at 170iterations 6.5708644E-04 1.1833191E-02 at 180iterations finished qdiffx linear iterations at : 08:55:13 total time elapsed so far: 13.90000 # loops : 180 mean,max change (kT/e) : 6.5708644E-04 1.1833191E-02 energy calculations done at 13.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.03000 DelPhi exited at 08:55:15 14.034u 0.316s 0:15.36 93.3% 0+0k 0+0io 0pf+0w