Wed Dec 21 14:21:00 PST 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 Wed Dec 21 2011 at 14:21:00 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 = 1957 !!! WARNING: PHE 153 has a net charge of -0.0320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6404030 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): -5.187000 35.04600 ymin,ymax (A): -3.634000 49.36100 zmin,zma (A): -24.41400 31.17600 x,y,z range (A): 40.23300 52.99500 55.59000 scale (grids/A): 0.6404030 object centre (A): 14.92950 22.86350 3.381001 number of atom coordinates read : 1957 total number of charged atoms : 1825 net assigned charge : 1.968007 assigned positive charge : 287.7691 centred at (gu) : 90.61243 92.30707 90.12098 assigned negative charge : -285.8013 centred at (gu) : 90.74158 92.45223 90.06528 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5530 nv = 96 ne = 84 npr = 40034 no. pairs analyzed = 40034 no. exposed pairs = 2444 no. arc points = 17325 no. surface atoms = 825 nbur = 1132 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 286 mr = 3109 m= 0 mr = 34 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.1700000 number of dielectric boundary points 2673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4927209E-09 8.2799474E-09 midg,1,midg; midg,igrid,midg 9.5573593E-09 -1.5842211E-08 1,midg,midg; igrid,midg,midg 1.2515378E-08 -9.1716466E-09 gauss-seidel spectral radius is 0.9873105 estimated iterations to convergence 73 setup time was (sec) 0.3500000 now iterating at: 14:21:01 rms-change max change #iterations 0.1235754 20.17825 at 10iterations 1.2183786E-02 2.122086 at 20iterations 1.2192201E-03 0.1819859 at 30iterations 1.1892207E-04 1.7883301E-02 at 40iterations 1.1744538E-05 1.7776489E-03 at 50iterations finished qdiffx linear iterations at : 14:21:05 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 1.1744538E-05 1.7776489E-03 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 14:21:05 4.366u 0.327s 0:05.47 85.5% 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 Dec 21 2011 at 14:21:05 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 = 1957 !!! WARNING: PHE 153 has a net charge of -0.0320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.921209 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): -5.187000 35.04600 ymin,ymax (A): -3.634000 49.36100 zmin,zma (A): -24.41400 31.17600 x,y,z range (A): 40.23300 52.99500 55.59000 scale (grids/A): 1.921209 object centre (A): 14.92950 22.86350 3.381001 number of atom coordinates read : 1957 total number of charged atoms : 1825 net assigned charge : 1.968007 assigned positive charge : 287.7691 centred at (gu) : 91.83758 96.92129 90.36279 assigned negative charge : -285.8013 centred at (gu) : 92.22488 97.35671 90.19601 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 59397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17325 grid for indexing accessible points = 1.400000 m= 22267 mr = 41180 m= 3478 mr = 17132 m= 157 mr = 2341 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 24589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14412 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) : 0.6404030 object centre at (A) : 14.92950 22.86350 3.381001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0469836E-02 9.0590566E-03 midg,1,midg; midg,igrid,midg 3.2031715E-02 -1.2555750E-02 1,midg,midg; igrid,midg,midg 8.6982800E-03 -6.4894906E-03 gauss-seidel spectral radius is 0.9985799 estimated iterations to convergence 210 setup time was (sec) 0.8300000 now iterating at: 14:21:07 rms-change max change #iterations 3.609764 162.8459 at 10iterations 1.666407 59.88668 at 20iterations 0.7721266 27.88466 at 30iterations 0.3573621 13.60139 at 40iterations 0.1634077 5.530458 at 50iterations 7.5533748E-02 2.783791 at 60iterations 3.4721728E-02 1.202477 at 70iterations 1.6058929E-02 0.5337372 at 80iterations 7.4052722E-03 0.2553225 at 90iterations 3.4124469E-03 0.1329532 at 100iterations 1.5832869E-03 5.9394836E-02 at 110iterations 7.2644959E-04 3.0239582E-02 at 120iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 7.2644959E-04 3.0239582E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 14:21:17 9.732u 0.596s 0:11.80 87.4% 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 Dec 21 2011 at 14:21:19 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 = 1957 !!! WARNING: PHE 153 has a net charge of -0.0320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.881813 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): -5.187000 35.04600 ymin,ymax (A): -3.634000 49.36100 zmin,zma (A): -24.41400 31.17600 x,y,z range (A): 40.23300 52.99500 55.59000 scale (grids/A): 2.881813 object centre (A): 14.92950 22.86350 3.381001 number of atom coordinates read : 1957 total number of charged atoms : 1825 net assigned charge : 1.968007 assigned positive charge : 287.7691 centred at (gu) : 92.75631 100.3819 90.54425 assigned negative charge : -285.8013 centred at (gu) : 93.33727 101.0352 90.29394 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 136999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17325 grid for indexing accessible points = 1.400000 m= 71203 mr = 99313 m= 27006 mr = 59396 m= 6394 mr = 22594 m= 758 mr = 5052 m= 32 mr = 481 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 55539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 14599 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) : 1.921209 object centre at (A) : 14.92950 22.86350 3.381001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.009555 -7.6413585E-04 midg,1,midg; midg,igrid,midg 0.3363140 -0.1630965 1,midg,midg; igrid,midg,midg 5.0576288E-02 -4.3116942E-02 gauss-seidel spectral radius is 0.9992302 estimated iterations to convergence 285 setup time was (sec) 1.060000 now iterating at: 14:21:22 rms-change max change #iterations 8.506154 422.5767 at 10iterations 4.879694 106.8872 at 20iterations 2.775540 59.76596 at 30iterations 1.578535 34.77280 at 40iterations 0.8976808 20.07523 at 50iterations 0.5088065 11.51918 at 60iterations 0.2886828 6.369995 at 70iterations 0.1637923 3.297157 at 80iterations 9.2699826E-02 1.791827 at 90iterations 5.2608121E-02 1.111925 at 100iterations 2.9767256E-02 0.5794635 at 110iterations 1.6892798E-02 0.3544445 at 120iterations 9.5909676E-03 0.1968274 at 130iterations 5.4297782E-03 0.1107216 at 140iterations 3.0786698E-03 5.7312012E-02 at 150iterations 1.7478531E-03 3.5940170E-02 at 160iterations 9.8907843E-04 1.8887997E-02 at 170iterations 5.6083273E-04 1.1369228E-02 at 180iterations finished qdiffx linear iterations at : 14:21:36 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 5.6083273E-04 1.1369228E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 14:21:40 15.487u 0.376s 0:21.23 74.6% 0+0k 0+0io 0pf+0w