Tue Oct 11 06:09:10 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 06:09:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 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: 0.7128268 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): -18.54300 26.10800 ymin,ymax (A): -12.25400 28.33800 zmin,zma (A): -3.122000 46.82000 x,y,z range (A): 44.65100 40.59200 49.94200 scale (grids/A): 0.7128268 object centre (A): 3.782499 8.042001 21.84900 number of atom coordinates read : 2124 total number of charged atoms : 1996 net assigned charge : 6.500008 assigned positive charge : 324.3239 centred at (gu) : 89.00060 89.62785 90.97254 assigned negative charge : -317.8241 centred at (gu) : 88.88411 89.65022 91.05372 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7205 nv = 96 ne = 84 npr = 43030 no. pairs analyzed = 43030 no. exposed pairs = 2536 no. arc points = 17060 no. surface atoms = 869 nbur = 1255 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4202 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1602 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0546678E-08 1.9794401E-08 midg,1,midg; midg,igrid,midg 8.1557125E-08 4.7327838E-08 1,midg,midg; igrid,midg,midg -5.0289306E-09 1.0619375E-07 gauss-seidel spectral radius is 0.9897400 estimated iterations to convergence 80 setup time was (sec) 0.5600000 now iterating at: 06:09:11 rms-change max change #iterations 0.2002817 25.63270 at 10iterations 2.5855001E-02 3.504891 at 20iterations 3.3874088E-03 0.4492044 at 30iterations 5.0739903E-04 6.7941666E-02 at 40iterations 1.0548202E-04 1.5535355E-02 at 50iterations finished qdiffx linear iterations at : 06:09:16 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 1.0548202E-04 1.5535355E-02 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 06:09:16 5.004u 0.439s 0:05.76 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 06:09:16 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 = 2124 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: 2.138481 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): -18.54300 26.10800 ymin,ymax (A): -12.25400 28.33800 zmin,zma (A): -3.122000 46.82000 x,y,z range (A): 44.65100 40.59200 49.94200 scale (grids/A): 2.138481 object centre (A): 3.782499 8.042001 21.84900 number of atom coordinates read : 2124 total number of charged atoms : 1996 net assigned charge : 6.500008 assigned positive charge : 324.3239 centred at (gu) : 87.00164 88.88336 92.91754 assigned negative charge : -317.8241 centred at (gu) : 86.65250 88.95050 93.16133 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17060 grid for indexing accessible points = 1.400000 m= 30643 mr = 55242 m= 5987 mr = 23389 m= 532 mr = 3964 m= 22 mr = 264 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 31212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15860 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) : 0.7128268 object centre at (A) : 3.782499 8.042001 21.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1399520E-02 5.6578469E-02 midg,1,midg; midg,igrid,midg 3.2057274E-02 6.7705479E-03 1,midg,midg; igrid,midg,midg 2.2687754E-02 3.0906070E-02 gauss-seidel spectral radius is 0.9988467 estimated iterations to convergence 233 setup time was (sec) 1.010000 now iterating at: 06:09:18 rms-change max change #iterations 4.704610 165.0495 at 10iterations 2.346937 70.15863 at 20iterations 1.171608 40.56160 at 30iterations 0.5839461 17.50797 at 40iterations 0.2919568 9.302556 at 50iterations 0.1457247 4.327017 at 60iterations 7.2913446E-02 2.376583 at 70iterations 3.6401141E-02 1.106857 at 80iterations 1.8132238E-02 0.5592213 at 90iterations 9.1237510E-03 0.2666931 at 100iterations 4.5722141E-03 0.1443443 at 110iterations 2.3185799E-03 7.4694633E-02 at 120iterations finished qdiffx linear iterations at : 06:09:29 total time elapsed so far: 12.02000 # loops : 120 mean,max change (kT/e) : 2.3185799E-03 7.4694633E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 06:09:29 12.186u 0.493s 0:12.99 97.5% 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 Tue Oct 11 2011 at 06:09:29 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 = 2124 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: 3.207721 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): -18.54300 26.10800 ymin,ymax (A): -12.25400 28.33800 zmin,zma (A): -3.122000 46.82000 x,y,z range (A): 44.65100 40.59200 49.94200 scale (grids/A): 3.207721 object centre (A): 3.782499 8.042001 21.84900 number of atom coordinates read : 2124 total number of charged atoms : 1996 net assigned charge : 6.500008 assigned positive charge : 324.3239 centred at (gu) : 85.50255 88.32504 94.37632 assigned negative charge : -317.8241 centred at (gu) : 84.97878 88.42570 94.74201 start vw surface at 0.1100000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 177041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17060 grid for indexing accessible points = 1.400000 m= 95861 mr = 132429 m= 39064 mr = 80179 m= 11487 mr = 32344 m= 2212 mr = 8844 m= 268 mr = 1593 m= 12 mr = 157 m= 0 mr = 5 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 70394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 15968 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) : 2.138481 object centre at (A) : 3.782499 8.042001 21.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3065753 0.6188217 midg,1,midg; midg,igrid,midg 0.2519820 3.7530575E-02 1,midg,midg; igrid,midg,midg 0.4717365 0.2881993 gauss-seidel spectral radius is 0.9992986 estimated iterations to convergence 298 setup time was (sec) 2.440000 now iterating at: 06:09:32 rms-change max change #iterations 10.44217 306.4898 at 10iterations 6.187912 150.2749 at 20iterations 3.644528 85.49495 at 30iterations 2.153328 48.10659 at 40iterations 1.264832 26.64199 at 50iterations 0.7440318 13.66339 at 60iterations 0.4359185 8.018469 at 70iterations 0.2558551 5.220100 at 80iterations 0.1500244 2.593740 at 90iterations 8.7902464E-02 1.789513 at 100iterations 5.1740371E-02 0.9905233 at 110iterations 3.0420214E-02 0.5104675 at 120iterations 1.7978232E-02 0.3278465 at 130iterations 1.0752929E-02 0.1809063 at 140iterations 6.5354174E-03 0.1204367 at 150iterations 4.0891673E-03 7.3304176E-02 at 160iterations 2.6769303E-03 4.8761427E-02 at 170iterations 1.8546015E-03 3.2956600E-02 at 180iterations finished qdiffx linear iterations at : 06:09:50 total time elapsed so far: 20.81000 # loops : 180 mean,max change (kT/e) : 1.8546015E-03 3.2956600E-02 energy calculations done at 20.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.98000 DelPhi exited at 06:09:51 20.985u 0.549s 0:21.84 98.5% 0+0k 0+0io 0pf+0w