Mon Oct 10 14:00:05 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 14:00:06 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 586 has a net charge of 1.4000 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: 0.6190766 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): -31.14300 17.45300 ymin,ymax (A): -23.70500 22.66900 zmin,zma (A): -12.44000 45.06500 x,y,z range (A): 48.59600 46.37400 57.50500 scale (grids/A): 0.6190766 object centre (A): -6.844999 -0.5180006 16.31250 number of atom coordinates read : 2580 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.52566 89.27785 89.52515 assigned negative charge : -388.8955 centred at (gu) : 88.40974 89.33137 89.40867 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6442 nv = 96 ne = 84 npr = 53402 no. pairs analyzed = 53402 no. exposed pairs = 3036 no. arc points = 21842 no. surface atoms = 1015 nbur = 1565 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 3556 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.3500000 number of dielectric boundary points 3141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2196 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8071 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4406874E-09 9.9867234E-09 midg,1,midg; midg,igrid,midg 8.3176506E-09 1.7787181E-10 1,midg,midg; igrid,midg,midg -5.5833520E-09 8.0025595E-09 gauss-seidel spectral radius is 0.9864827 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 14:00:07 rms-change max change #iterations 0.1262481 21.72833 at 10iterations 1.1374806E-02 1.813110 at 20iterations 1.0624053E-03 0.1399479 at 30iterations 9.8040568E-05 1.4389992E-02 at 40iterations 9.0265030E-06 1.3113022E-03 at 50iterations finished qdiffx linear iterations at : 14:00:09 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 9.0265030E-06 1.3113022E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:00:10 3.376u 0.171s 0:03.95 89.6% 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 Mon Oct 10 2011 at 14:00:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 586 has a net charge of 1.4000 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: 1.857230 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): -31.14300 17.45300 ymin,ymax (A): -23.70500 22.66900 zmin,zma (A): -12.44000 45.06500 x,y,z range (A): 48.59600 46.37400 57.50500 scale (grids/A): 1.857230 object centre (A): -6.844999 -0.5180006 16.31250 number of atom coordinates read : 2580 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.57634 87.83287 88.57509 assigned negative charge : -388.8955 centred at (gu) : 85.22912 87.99384 88.22592 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21842 grid for indexing accessible points = 1.400000 m= 23830 mr = 48527 m= 3342 mr = 17453 m= 145 mr = 2022 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3544 time to turn everything in is 0.5100000 number of dielectric boundary points 29080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19349 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) : 0.6190766 object centre at (A) : -6.844999 -0.5180006 16.31250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6071305E-02 2.5840882E-02 midg,1,midg; midg,igrid,midg 1.3517356E-02 1.6613448E-03 1,midg,midg; igrid,midg,midg -4.0966794E-03 3.7958071E-02 gauss-seidel spectral radius is 0.9985618 estimated iterations to convergence 209 setup time was (sec) 0.8000000 now iterating at: 14:00:11 rms-change max change #iterations 4.024153 183.8378 at 10iterations 1.848971 63.26699 at 20iterations 0.8453138 30.21886 at 30iterations 0.3885040 12.13808 at 40iterations 0.1788455 6.174968 at 50iterations 8.2056813E-02 2.863117 at 60iterations 3.7675053E-02 1.475180 at 70iterations 1.7204290E-02 0.5209732 at 80iterations 7.9276934E-03 0.2757645 at 90iterations 3.6431344E-03 0.1137104 at 100iterations 1.6697431E-03 4.9571991E-02 at 110iterations 7.6884753E-04 2.4951935E-02 at 120iterations finished qdiffx linear iterations at : 14:00:17 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 7.6884753E-04 2.4951935E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 14:00:18 7.385u 0.217s 0:08.08 93.9% 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 14:00:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 586 has a net charge of 1.4000 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: 2.785845 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): -31.14300 17.45300 ymin,ymax (A): -23.70500 22.66900 zmin,zma (A): -12.44000 45.06500 x,y,z range (A): 48.59600 46.37400 57.50500 scale (grids/A): 2.785845 object centre (A): -6.844999 -0.5180006 16.31250 number of atom coordinates read : 2580 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.36434 86.74917 87.86268 assigned negative charge : -388.8955 centred at (gu) : 82.84360 86.99063 87.33884 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 161994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21842 grid for indexing accessible points = 1.400000 m= 78760 mr = 117738 m= 26482 mr = 64476 m= 5928 mr = 21215 m= 741 mr = 4418 m= 33 mr = 463 m= 0 mr = 12 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 12299 time to turn everything in is 1.270000 number of dielectric boundary points 65616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 19723 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) : 1.857230 object centre at (A) : -6.844999 -0.5180006 16.31250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9555648E-02 0.3596464 midg,1,midg; midg,igrid,midg 0.1598736 9.8983739E-03 1,midg,midg; igrid,midg,midg -5.0129704E-02 0.5044599 gauss-seidel spectral radius is 0.9992322 estimated iterations to convergence 285 setup time was (sec) 1.580000 now iterating at: 14:00:20 rms-change max change #iterations 9.455313 323.3051 at 10iterations 5.431872 136.8849 at 20iterations 3.101254 68.25397 at 30iterations 1.765208 39.45396 at 40iterations 1.004106 19.13737 at 50iterations 0.5735422 11.54870 at 60iterations 0.3260081 6.461650 at 70iterations 0.1852026 3.663229 at 80iterations 0.1053513 2.054020 at 90iterations 5.9984855E-02 1.106548 at 100iterations 3.4044143E-02 0.7074203 at 110iterations 1.9362714E-02 0.4064445 at 120iterations 1.0997397E-02 0.2376289 at 130iterations 6.2477863E-03 0.1257477 at 140iterations 3.5569340E-03 7.2987556E-02 at 150iterations 2.0238210E-03 3.9450645E-02 at 160iterations 1.1553944E-03 2.1566391E-02 at 170iterations 6.5863831E-04 1.3655663E-02 at 180iterations finished qdiffx linear iterations at : 14:00:30 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 6.5863831E-04 1.3655663E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 14:00:31 12.433u 0.206s 0:13.16 95.9% 0+0k 0+0io 0pf+0w