Sat Oct 15 13:37:49 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 Sat Oct 15 2011 at 13:37:49 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7397557 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): -20.80000 24.85500 ymin,ymax (A): -7.988000 35.84500 zmin,zma (A): -3.500000 44.62400 x,y,z range (A): 45.65500 43.83300 48.12400 scale (grids/A): 0.7397557 object centre (A): 2.027499 13.92850 20.56200 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 88.72422 90.64766 90.11668 assigned negative charge : -322.8520 centred at (gu) : 88.76435 90.72487 90.28796 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8086 nv = 96 ne = 84 npr = 43658 no. pairs analyzed = 43658 no. exposed pairs = 2732 no. arc points = 19238 no. surface atoms = 923 nbur = 1192 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 578 mr = 4501 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1800000 number of dielectric boundary points 4055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1522 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5304782E-08 -2.8810410E-07 midg,1,midg; midg,igrid,midg -2.4192593E-08 -2.0730864E-07 1,midg,midg; igrid,midg,midg -7.9756298E-08 -1.1542335E-07 gauss-seidel spectral radius is 0.9904787 estimated iterations to convergence 83 setup time was (sec) 0.4000000 now iterating at: 13:37:50 rms-change max change #iterations 0.2397845 32.29563 at 10iterations 3.2603327E-02 4.386230 at 20iterations 4.3157474E-03 0.5414104 at 30iterations 5.8446394E-04 7.2604179E-02 at 40iterations 7.9537116E-05 9.7179413E-03 at 50iterations finished qdiffx linear iterations at : 13:37:56 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 7.9537116E-05 9.7179413E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 13:37:57 3.914u 0.262s 0:07.22 57.7% 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 Sat Oct 15 2011 at 13:37:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.219267 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): -20.80000 24.85500 ymin,ymax (A): -7.988000 35.84500 zmin,zma (A): -3.500000 44.62400 x,y,z range (A): 45.65500 43.83300 48.12400 scale (grids/A): 2.219267 object centre (A): 2.027499 13.92850 20.56200 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 86.17290 91.94324 90.34985 assigned negative charge : -322.8520 centred at (gu) : 86.29295 92.17452 90.86376 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19238 grid for indexing accessible points = 1.400000 m= 34105 mr = 57994 m= 7197 mr = 25734 m= 729 mr = 4919 m= 23 mr = 369 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 291 time to turn everything in is 0.4500000 number of dielectric boundary points 37051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 15738 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) : 0.7397557 object centre at (A) : 2.027499 13.92850 20.56200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4421645E-03 -0.1290141 midg,1,midg; midg,igrid,midg -2.6613114E-02 -3.2859344E-02 1,midg,midg; igrid,midg,midg -1.2372332E-02 4.4922098E-03 gauss-seidel spectral radius is 0.9989256 estimated iterations to convergence 241 setup time was (sec) 0.7100000 now iterating at: 13:37:58 rms-change max change #iterations 5.079262 208.1198 at 10iterations 2.582875 76.59129 at 20iterations 1.312592 40.24067 at 30iterations 0.6682957 19.77135 at 40iterations 0.3408906 10.39040 at 50iterations 0.1737877 4.820875 at 60iterations 8.8377476E-02 2.656548 at 70iterations 4.4975556E-02 1.436769 at 80iterations 2.3111302E-02 0.6292782 at 90iterations 1.1723819E-02 0.3260498 at 100iterations 5.9674028E-03 0.1781157 at 110iterations 3.0492137E-03 9.0686798E-02 at 120iterations finished qdiffx linear iterations at : 13:38:11 total time elapsed so far: 8.600000 # loops : 120 mean,max change (kT/e) : 3.0492137E-03 9.0686798E-02 energy calculations done at 8.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 13:38:11 8.736u 0.296s 0:14.56 61.9% 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 Sat Oct 15 2011 at 13:38:12 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.328901 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): -20.80000 24.85500 ymin,ymax (A): -7.988000 35.84500 zmin,zma (A): -3.500000 44.62400 x,y,z range (A): 45.65500 43.83300 48.12400 scale (grids/A): 3.328901 object centre (A): 2.027499 13.92850 20.56200 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 84.25926 92.91487 90.52483 assigned negative charge : -322.8520 centred at (gu) : 84.43943 93.26173 91.29574 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 193340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19238 grid for indexing accessible points = 1.400000 m= 103528 mr = 139570 m= 44693 mr = 85590 m= 13748 mr = 36854 m= 3003 mr = 10703 m= 409 mr = 2216 m= 27 mr = 245 m= 0 mr = 15 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 913 time to turn everything in is 1.330000 number of dielectric boundary points 83555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 15808 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) : 2.219267 object centre at (A) : 2.027499 13.92850 20.56200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7437171E-02 -1.194674 midg,1,midg; midg,igrid,midg -0.2334006 -0.1617482 1,midg,midg; igrid,midg,midg -0.2201067 3.9089654E-02 gauss-seidel spectral radius is 0.9993214 estimated iterations to convergence 303 setup time was (sec) 1.610000 now iterating at: 13:38:15 rms-change max change #iterations 10.95781 323.3015 at 10iterations 6.477008 127.0701 at 20iterations 3.831316 81.09103 at 30iterations 2.258410 38.13411 at 40iterations 1.334963 23.43256 at 50iterations 0.7840871 13.68621 at 60iterations 0.4613430 7.367963 at 70iterations 0.2720830 4.617867 at 80iterations 0.1597281 2.516999 at 90iterations 9.4106197E-02 1.468861 at 100iterations 5.5221789E-02 0.9703021 at 110iterations 3.2501236E-02 0.4870949 at 120iterations 1.9099833E-02 0.3117867 at 130iterations 1.1230705E-02 0.1864481 at 140iterations 6.6291578E-03 0.1125984 at 150iterations 3.8884231E-03 6.1599970E-02 at 160iterations 2.2910922E-03 3.6819458E-02 at 170iterations 1.3458522E-03 2.2902489E-02 at 180iterations finished qdiffx linear iterations at : 13:38:37 total time elapsed so far: 14.71000 # loops : 180 mean,max change (kT/e) : 1.3458522E-03 2.2902489E-02 energy calculations done at 14.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.84000 DelPhi exited at 13:38:38 14.841u 0.268s 0:26.08 57.8% 0+0k 0+0io 0pf+0w