Tue Oct 11 08:08:15 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 Tue Oct 11 2011 at 08:08:15 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 = 2335 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6419851 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): -22.84800 25.16600 ymin,ymax (A): 21.30700 76.76000 zmin,zma (A): 2.067000 51.47100 x,y,z range (A): 48.01400 55.45300 49.40400 scale (grids/A): 0.6419851 object centre (A): 1.159000 49.03350 26.76900 number of atom coordinates read : 2335 total number of charged atoms : 2197 net assigned charge : 4.500012 assigned positive charge : 350.0653 centred at (gu) : 91.21973 87.99348 92.02522 assigned negative charge : -345.5659 centred at (gu) : 91.02320 88.04301 91.96623 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6564 nv = 96 ne = 84 npr = 47030 no. pairs analyzed = 47030 no. exposed pairs = 3126 no. arc points = 21786 no. surface atoms = 1041 nbur = 1294 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3438 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.2800000 number of dielectric boundary points 3427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2243 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2072688E-11 1.9567819E-08 midg,1,midg; midg,igrid,midg 1.7910891E-08 7.0544043E-10 1,midg,midg; igrid,midg,midg -1.1802127E-08 3.5414491E-08 gauss-seidel spectral radius is 0.9874097 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 08:08:16 rms-change max change #iterations 0.1382536 24.39488 at 10iterations 1.3450440E-02 1.980394 at 20iterations 1.4306362E-03 0.2009239 at 30iterations 1.9932870E-04 3.8558006E-02 at 40iterations 5.4291497E-05 1.2796402E-02 at 50iterations finished qdiffx linear iterations at : 08:08:20 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 5.4291497E-05 1.2796402E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 08:08:20 4.466u 0.433s 0:05.19 94.2% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 08:08:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.925955 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): -22.84800 25.16600 ymin,ymax (A): 21.30700 76.76000 zmin,zma (A): 2.067000 51.47100 x,y,z range (A): 48.01400 55.45300 49.40400 scale (grids/A): 1.925955 object centre (A): 1.159000 49.03350 26.76900 number of atom coordinates read : 2335 total number of charged atoms : 2197 net assigned charge : 4.500012 assigned positive charge : 350.0653 centred at (gu) : 93.65902 83.97995 96.07524 assigned negative charge : -345.5659 centred at (gu) : 93.06956 84.12888 95.89857 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21786 grid for indexing accessible points = 1.400000 m= 24952 mr = 47794 m= 3827 mr = 17816 m= 282 mr = 2236 m= 5 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2861 time to turn everything in is 0.5700000 number of dielectric boundary points 31652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 3.930000 number of grid points assigned charge 17361 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) : 0.6419851 object centre at (A) : 1.159000 49.03350 26.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0523396E-04 3.3129353E-02 midg,1,midg; midg,igrid,midg 5.1593397E-02 1.4967290E-02 1,midg,midg; igrid,midg,midg -1.8136965E-02 3.1231588E-02 gauss-seidel spectral radius is 0.9986370 estimated iterations to convergence 215 setup time was (sec) 4.120000 now iterating at: 08:08:25 rms-change max change #iterations 4.027921 184.9021 at 10iterations 1.880684 64.28963 at 20iterations 0.8788733 31.04856 at 30iterations 0.4120874 13.76859 at 40iterations 0.1928516 6.363487 at 50iterations 9.0281762E-02 3.414810 at 60iterations 4.2040762E-02 1.339676 at 70iterations 1.9765785E-02 0.6137228 at 80iterations 9.2632640E-03 0.2917366 at 90iterations 4.3536131E-03 0.1410046 at 100iterations 2.0525048E-03 7.1865082E-02 at 110iterations 9.7762293E-04 3.5114288E-02 at 120iterations finished qdiffx linear iterations at : 08:08:35 total time elapsed so far: 13.69000 # loops : 120 mean,max change (kT/e) : 9.7762293E-04 3.5114288E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 08:08:35 13.865u 0.465s 0:14.91 96.0% 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 Tue Oct 11 2011 at 08:08:35 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 = 2335 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.888933 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): -22.84800 25.16600 ymin,ymax (A): 21.30700 76.76000 zmin,zma (A): 2.067000 51.47100 x,y,z range (A): 48.01400 55.45300 49.40400 scale (grids/A): 2.888933 object centre (A): 1.159000 49.03350 26.76900 number of atom coordinates read : 2335 total number of charged atoms : 2197 net assigned charge : 4.500012 assigned positive charge : 350.0653 centred at (gu) : 95.48841 80.96992 99.11282 assigned negative charge : -345.5659 centred at (gu) : 94.60427 81.19321 98.84789 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 162999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21786 grid for indexing accessible points = 1.400000 m= 80743 mr = 116018 m= 28659 mr = 64903 m= 6644 mr = 22372 m= 1063 mr = 4713 m= 111 mr = 736 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 10045 time to turn everything in is 1.520000 number of dielectric boundary points 71412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 17576 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) : 1.925955 object centre at (A) : 1.159000 49.03350 26.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5959149E-02 0.3309799 midg,1,midg; midg,igrid,midg 0.5380018 0.3893270 1,midg,midg; igrid,midg,midg -0.1745196 0.2968719 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.910000 now iterating at: 08:08:38 rms-change max change #iterations 9.692445 405.0713 at 10iterations 5.730923 138.3964 at 20iterations 3.375177 91.57820 at 30iterations 1.972105 42.61391 at 40iterations 1.150255 24.98655 at 50iterations 0.6696990 14.89492 at 60iterations 0.3892007 7.306479 at 70iterations 0.2252762 4.682674 at 80iterations 0.1307668 2.578236 at 90iterations 7.5338408E-02 1.516529 at 100iterations 4.3616567E-02 0.8840418 at 110iterations 2.5188994E-02 0.4865723 at 120iterations 1.4567640E-02 0.2800827 at 130iterations 8.4313508E-03 0.1569366 at 140iterations 4.9007684E-03 9.5590591E-02 at 150iterations 2.8649189E-03 6.0389519E-02 at 160iterations 1.6972169E-03 3.6373138E-02 at 170iterations 1.0260622E-03 2.2809982E-02 at 180iterations finished qdiffx linear iterations at : 08:08:54 total time elapsed so far: 17.85000 # loops : 180 mean,max change (kT/e) : 1.0260622E-03 2.2809982E-02 energy calculations done at 17.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.02000 DelPhi exited at 08:08:55 18.027u 0.460s 0:19.03 97.1% 0+0k 0+0io 0pf+0w