Tue Oct 11 06:16:14 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+sph2.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 = amb2.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 06:16:14 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2007 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7318778 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): -19.51600 23.73700 ymin,ymax (A): -10.98900 27.42500 zmin,zma (A): -2.923000 45.71900 x,y,z range (A): 43.25300 38.41400 48.64200 scale (grids/A): 0.7318778 object centre (A): 2.110500 8.218000 21.39800 number of atom coordinates read : 2007 total number of charged atoms : 1890 net assigned charge : 7.025011 assigned positive charge : 309.0352 centred at (gu) : 89.81651 89.30596 91.12250 assigned negative charge : -302.0101 centred at (gu) : 89.63531 89.32607 91.22312 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7524 nv = 96 ne = 84 npr = 39293 no. pairs analyzed = 39293 no. exposed pairs = 2566 no. arc points = 17787 no. surface atoms = 864 nbur = 1143 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 542 mr = 4292 m= 8 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1597 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7963 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5061411E-07 2.6456455E-08 midg,1,midg; midg,igrid,midg 1.3769048E-07 7.8235296E-08 1,midg,midg; igrid,midg,midg -4.6228649E-08 2.4056030E-07 gauss-seidel spectral radius is 0.9902591 estimated iterations to convergence 82 setup time was (sec) 0.4800000 now iterating at: 06:16:15 rms-change max change #iterations 0.2297271 32.90421 at 10iterations 2.9939128E-02 4.387921 at 20iterations 4.0908018E-03 0.4889526 at 30iterations 6.4183521E-04 8.2275391E-02 at 40iterations 1.3867400E-04 1.7436981E-02 at 50iterations finished qdiffx linear iterations at : 06:16:17 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.3867400E-04 1.7436981E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 06:16:18 3.262u 0.186s 0:03.84 89.5% 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 06:16:18 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2007 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.195633 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): -19.51600 23.73700 ymin,ymax (A): -10.98900 27.42500 zmin,zma (A): -2.923000 45.71900 x,y,z range (A): 43.25300 38.41400 48.64200 scale (grids/A): 2.195633 object centre (A): 2.110500 8.218000 21.39800 number of atom coordinates read : 2007 total number of charged atoms : 1890 net assigned charge : 7.025011 assigned positive charge : 309.0352 centred at (gu) : 89.44956 87.91814 93.36771 assigned negative charge : -302.0101 centred at (gu) : 88.90590 87.97796 93.66943 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 33759 mr = 55369 m= 7433 mr = 25887 m= 773 mr = 5065 m= 21 mr = 395 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 33913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15048 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) : 0.7318778 object centre at (A) : 2.110500 8.218000 21.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8496248E-02 5.4593277E-03 midg,1,midg; midg,igrid,midg 4.4872828E-02 2.0249056E-02 1,midg,midg; igrid,midg,midg 2.3039317E-02 5.5757083E-02 gauss-seidel spectral radius is 0.9988959 estimated iterations to convergence 238 setup time was (sec) 0.8800000 now iterating at: 06:16:19 rms-change max change #iterations 4.861624 207.4860 at 10iterations 2.449737 83.00184 at 20iterations 1.247166 35.70781 at 30iterations 0.6343024 19.14440 at 40iterations 0.3204030 9.961533 at 50iterations 0.1626535 4.890688 at 60iterations 8.2065679E-02 2.432148 at 70iterations 4.1700400E-02 1.217283 at 80iterations 2.1115525E-02 0.6822791 at 90iterations 1.0731827E-02 0.3117447 at 100iterations 5.5002156E-03 0.1765366 at 110iterations 2.8374046E-03 8.6712837E-02 at 120iterations finished qdiffx linear iterations at : 06:16:26 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 2.8374046E-03 8.6712837E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 06:16:26 7.613u 0.204s 0:08.34 93.6% 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 Tue Oct 11 2011 at 06:16:26 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2007 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.293450 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): -19.51600 23.73700 ymin,ymax (A): -10.98900 27.42500 zmin,zma (A): -2.923000 45.71900 x,y,z range (A): 43.25300 38.41400 48.64200 scale (grids/A): 3.293450 object centre (A): 2.110500 8.218000 21.39800 number of atom coordinates read : 2007 total number of charged atoms : 1890 net assigned charge : 7.025011 assigned positive charge : 309.0352 centred at (gu) : 89.17436 86.87722 95.05165 assigned negative charge : -302.0101 centred at (gu) : 88.35892 86.96703 95.50429 start vw surface at 0.1400000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 180633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 102311 mr = 133047 m= 45288 mr = 85437 m= 14290 mr = 37378 m= 3095 mr = 11160 m= 384 mr = 2274 m= 13 mr = 248 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 76468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 15120 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) : 2.195633 object centre at (A) : 2.110500 8.218000 21.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1598409 -1.0043747E-02 midg,1,midg; midg,igrid,midg 0.3486127 0.1342293 1,midg,midg; igrid,midg,midg 0.4593353 0.4344556 gauss-seidel spectral radius is 0.9993139 estimated iterations to convergence 301 setup time was (sec) 2.230000 now iterating at: 06:16:29 rms-change max change #iterations 10.74256 344.9670 at 10iterations 6.448755 128.7334 at 20iterations 3.857217 75.65876 at 30iterations 2.299556 43.84598 at 40iterations 1.367512 25.54551 at 50iterations 0.8104946 14.46457 at 60iterations 0.4798352 8.585720 at 70iterations 0.2847323 4.723794 at 80iterations 0.1684776 3.062897 at 90iterations 9.9384673E-02 1.895258 at 100iterations 5.8837935E-02 1.071004 at 110iterations 3.4823902E-02 0.6174440 at 120iterations 2.0766342E-02 0.3580890 at 130iterations 1.2506656E-02 0.2261391 at 140iterations 7.6497812E-03 0.1471443 at 150iterations 4.8264470E-03 8.6318970E-02 at 160iterations 3.1873961E-03 5.3459167E-02 at 170iterations 2.2333493E-03 3.8574219E-02 at 180iterations finished qdiffx linear iterations at : 06:16:39 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 2.2333493E-03 3.8574219E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 06:16:40 12.544u 0.247s 0:13.08 97.7% 0+0k 0+0io 0pf+0w