Tue Oct 11 06:37:28 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 06:37:28 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 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: 0.7068822 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): -20.88700 24.63400 ymin,ymax (A): -28.57500 10.99100 zmin,zma (A): -13.54300 36.81900 x,y,z range (A): 45.52100 39.56600 50.36200 scale (grids/A): 0.7068822 object centre (A): 1.873501 -8.792001 11.63800 number of atom coordinates read : 2037 total number of charged atoms : 1909 net assigned charge : 7.500009 assigned positive charge : 309.4421 centred at (gu) : 90.14789 90.50195 89.49462 assigned negative charge : -301.9422 centred at (gu) : 89.97155 90.47947 89.46335 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6894 nv = 96 ne = 84 npr = 40958 no. pairs analyzed = 40958 no. exposed pairs = 2441 no. arc points = 16817 no. surface atoms = 830 nbur = 1207 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3943 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2900000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7744 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2240452E-08 7.0089335E-08 midg,1,midg; midg,igrid,midg 4.7166342E-08 8.0328746E-08 1,midg,midg; igrid,midg,midg -2.1660432E-08 1.4851611E-07 gauss-seidel spectral radius is 0.9895632 estimated iterations to convergence 80 setup time was (sec) 0.5500000 now iterating at: 06:37:29 rms-change max change #iterations 0.1983528 28.13511 at 10iterations 2.4430027E-02 3.112210 at 20iterations 3.1043645E-03 0.4740505 at 30iterations 4.2829581E-04 5.7273865E-02 at 40iterations 7.2934490E-05 9.2363358E-03 at 50iterations finished qdiffx linear iterations at : 06:37:32 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 7.2934490E-05 9.2363358E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 06:37:32 3.541u 0.159s 0:04.06 90.8% 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 06:37:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 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: 2.120646 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): -20.88700 24.63400 ymin,ymax (A): -28.57500 10.99100 zmin,zma (A): -13.54300 36.81900 x,y,z range (A): 45.52100 39.56600 50.36200 scale (grids/A): 2.120646 object centre (A): 1.873501 -8.792001 11.63800 number of atom coordinates read : 2037 total number of charged atoms : 1909 net assigned charge : 7.500009 assigned positive charge : 309.4421 centred at (gu) : 90.44365 91.50598 88.48380 assigned negative charge : -301.9422 centred at (gu) : 89.91490 91.43853 88.39019 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16817 grid for indexing accessible points = 1.400000 m= 29229 mr = 51962 m= 5615 mr = 22183 m= 567 mr = 3756 m= 18 mr = 321 m= 0 mr = 9 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 132 time to turn everything in is 0.5800000 number of dielectric boundary points 30324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15158 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) : 0.7068822 object centre at (A) : 1.873501 -8.792001 11.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3066810E-02 4.6689525E-02 midg,1,midg; midg,igrid,midg 6.3909008E-03 3.4217823E-02 1,midg,midg; igrid,midg,midg 1.8366221E-02 4.2752475E-02 gauss-seidel spectral radius is 0.9988253 estimated iterations to convergence 231 setup time was (sec) 0.8700000 now iterating at: 06:37:34 rms-change max change #iterations 4.534105 230.8208 at 10iterations 2.238621 92.44132 at 20iterations 1.107636 37.51586 at 30iterations 0.5495946 17.49332 at 40iterations 0.2725244 8.420929 at 50iterations 0.1347370 4.358797 at 60iterations 6.6987351E-02 1.946385 at 70iterations 3.3063225E-02 0.9722347 at 80iterations 1.6457701E-02 0.5004425 at 90iterations 8.1846323E-03 0.2581215 at 100iterations 4.0578824E-03 0.1199188 at 110iterations 2.0299035E-03 6.1082363E-02 at 120iterations finished qdiffx linear iterations at : 06:37:41 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.0299035E-03 6.1082363E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 06:37:41 7.986u 0.230s 0:08.52 96.3% 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 Tue Oct 11 2011 at 06:37:41 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 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: 3.180970 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): -20.88700 24.63400 ymin,ymax (A): -28.57500 10.99100 zmin,zma (A): -13.54300 36.81900 x,y,z range (A): 45.52100 39.56600 50.36200 scale (grids/A): 3.180970 object centre (A): 1.873501 -8.792001 11.63800 number of atom coordinates read : 2037 total number of charged atoms : 1909 net assigned charge : 7.500009 assigned positive charge : 309.4421 centred at (gu) : 90.66553 92.25909 87.72566 assigned negative charge : -301.9422 centred at (gu) : 89.87232 92.15777 87.58540 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 168787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16817 grid for indexing accessible points = 1.400000 m= 91055 mr = 125183 m= 36946 mr = 75781 m= 10784 mr = 30521 m= 2200 mr = 8441 m= 315 mr = 1616 m= 28 mr = 240 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 1.830000 number of dielectric boundary points 68317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 15272 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) : 2.120646 object centre at (A) : 1.873501 -8.792001 11.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6698513 0.3717850 midg,1,midg; midg,igrid,midg 2.8837493E-02 0.2790037 1,midg,midg; igrid,midg,midg 0.2950438 0.3170348 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 2.150000 now iterating at: 06:37:43 rms-change max change #iterations 10.11618 362.7569 at 10iterations 5.948411 119.5782 at 20iterations 3.500825 81.85672 at 30iterations 2.052524 41.75766 at 40iterations 1.202326 21.75233 at 50iterations 0.7041646 12.58716 at 60iterations 0.4123040 8.379860 at 70iterations 0.2407133 4.119758 at 80iterations 0.1407304 2.565503 at 90iterations 8.1930563E-02 1.586595 at 100iterations 4.7931306E-02 0.9613934 at 110iterations 2.8018029E-02 0.5378860 at 120iterations 1.6397821E-02 0.2765942 at 130iterations 9.6682087E-03 0.1558161 at 140iterations 5.7677953E-03 0.1097412 at 150iterations 3.4632620E-03 6.4499855E-02 at 160iterations 2.1483658E-03 3.8692474E-02 at 170iterations 1.3896232E-03 2.4114609E-02 at 180iterations finished qdiffx linear iterations at : 06:37:56 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 1.3896232E-03 2.4114609E-02 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.94000 DelPhi exited at 06:37:57 14.946u 0.231s 0:15.61 97.1% 0+0k 0+0io 0pf+0w