Sun Oct 9 09:55:43 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 Sun Oct 9 2011 at 09:55:43 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5824321 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): 35.11300 90.00200 ymin,ymax (A): 7.937000 69.06001 zmin,zma (A): 44.87500 95.02900 x,y,z range (A): 54.88900 61.12300 50.15400 scale (grids/A): 0.5824321 object centre (A): 62.55750 38.49850 69.95200 number of atom coordinates read : 2698 total number of charged atoms : 2536 net assigned charge : -5.999979 assigned positive charge : 385.3094 centred at (gu) : 88.11854 89.68189 89.85019 assigned negative charge : -391.3109 centred at (gu) : 88.16930 89.69949 90.07324 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6192 nv = 96 ne = 84 npr = 53991 no. pairs analyzed = 53991 no. exposed pairs = 3691 no. arc points = 26536 no. surface atoms = 1242 nbur = 1456 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 349 mr = 3092 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2481 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2140757E-09 -6.0240644E-09 midg,1,midg; midg,igrid,midg -1.1581667E-09 -1.6886404E-09 1,midg,midg; igrid,midg,midg -5.6430383E-10 -1.6368871E-09 gauss-seidel spectral radius is 0.9847742 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 09:55:44 rms-change max change #iterations 9.3190894E-02 15.62686 at 10iterations 7.3140427E-03 1.191976 at 20iterations 5.8054447E-04 8.6318970E-02 at 30iterations 4.7077330E-05 7.2860718E-03 at 40iterations 3.9186211E-06 5.7601929E-04 at 50iterations finished qdiffx linear iterations at : 09:55:47 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.9186211E-06 5.7601929E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 09:55:47 3.467u 0.184s 0:03.90 93.3% 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 Sun Oct 9 2011 at 09:55:47 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.747296 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): 35.11300 90.00200 ymin,ymax (A): 7.937000 69.06001 zmin,zma (A): 44.87500 95.02900 x,y,z range (A): 54.88900 61.12300 50.15400 scale (grids/A): 1.747296 object centre (A): 62.55750 38.49850 69.95200 number of atom coordinates read : 2698 total number of charged atoms : 2536 net assigned charge : -5.999979 assigned positive charge : 385.3094 centred at (gu) : 84.35509 89.04482 89.54972 assigned negative charge : -391.3109 centred at (gu) : 84.50800 89.09857 90.21975 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26536 grid for indexing accessible points = 1.400000 m= 22390 mr = 44200 m= 3242 mr = 15420 m= 138 mr = 1800 m= 0 mr = 18 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 629 time to turn everything in is 0.3400000 number of dielectric boundary points 31797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19794 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) : 0.5824321 object centre at (A) : 62.55750 38.49850 69.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6588918E-03 -3.6350999E-02 midg,1,midg; midg,igrid,midg -9.9975606E-03 -7.9677450E-03 1,midg,midg; igrid,midg,midg 1.0081417E-02 -1.1521732E-02 gauss-seidel spectral radius is 0.9984118 estimated iterations to convergence 199 setup time was (sec) 0.5600000 now iterating at: 09:55:48 rms-change max change #iterations 3.580328 160.7813 at 10iterations 1.567109 62.34941 at 20iterations 0.6900626 25.44308 at 30iterations 0.3041847 10.02639 at 40iterations 0.1341118 4.657017 at 50iterations 5.9040189E-02 1.965531 at 60iterations 2.6015332E-02 0.9800282 at 70iterations 1.1463186E-02 0.4016991 at 80iterations 5.0658132E-03 0.1771488 at 90iterations 2.2387058E-03 7.8773499E-02 at 100iterations 9.8202995E-04 3.5335541E-02 at 110iterations 4.3589005E-04 1.4938354E-02 at 120iterations finished qdiffx linear iterations at : 09:55:55 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 4.3589005E-04 1.4938354E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 09:55:56 8.041u 0.227s 0:08.59 96.1% 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 Sun Oct 9 2011 at 09:55:56 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.620944 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): 35.11300 90.00200 ymin,ymax (A): 7.937000 69.06001 zmin,zma (A): 44.87500 95.02900 x,y,z range (A): 54.88900 61.12300 50.15400 scale (grids/A): 2.620944 object centre (A): 62.55750 38.49850 69.95200 number of atom coordinates read : 2698 total number of charged atoms : 2536 net assigned charge : -5.999979 assigned positive charge : 385.3094 centred at (gu) : 81.53246 88.56708 89.32454 assigned negative charge : -391.3109 centred at (gu) : 81.76186 88.64780 90.32975 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26536 grid for indexing accessible points = 1.400000 m= 73396 mr = 108325 m= 25113 mr = 57400 m= 5555 mr = 19219 m= 628 mr = 3896 m= 18 mr = 321 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2105 time to turn everything in is 0.8400000 number of dielectric boundary points 71601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20279 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) : 1.747296 object centre at (A) : 62.55750 38.49850 69.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6937514E-02 -0.4740311 midg,1,midg; midg,igrid,midg -0.1138999 -8.7811433E-02 1,midg,midg; igrid,midg,midg 0.1408091 -0.2197202 gauss-seidel spectral radius is 0.9992023 estimated iterations to convergence 280 setup time was (sec) 1.090000 now iterating at: 09:55:57 rms-change max change #iterations 8.926636 306.9657 at 10iterations 5.165377 132.6427 at 20iterations 2.959110 68.38767 at 30iterations 1.691492 44.48440 at 40iterations 0.9617221 21.54577 at 50iterations 0.5445387 10.98534 at 60iterations 0.3075762 6.897544 at 70iterations 0.1736865 3.499817 at 80iterations 9.7883709E-02 2.157610 at 90iterations 5.5342324E-02 1.137278 at 100iterations 3.1076577E-02 0.6151991 at 110iterations 1.7544284E-02 0.3352264 at 120iterations 9.8480396E-03 0.1853914 at 130iterations 5.5426094E-03 0.1045723 at 140iterations 3.1260042E-03 6.0758591E-02 at 150iterations 1.7595286E-03 3.4782410E-02 at 160iterations 9.9323504E-04 2.0454407E-02 at 170iterations 5.6030549E-04 1.1720657E-02 at 180iterations finished qdiffx linear iterations at : 09:56:09 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 5.6030549E-04 1.1720657E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 09:56:09 13.016u 0.236s 0:13.53 97.8% 0+0k 0+0io 0pf+0w