Wed Feb 15 08:55:59 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:00 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 = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5482236 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): 9.401000 71.95800 ymin,ymax (A): -1.397000 63.54000 zmin,zma (A): -5.290000 37.29200 x,y,z range (A): 62.55700 64.93700 42.58200 scale (grids/A): 0.5482236 object centre (A): 40.67950 31.07150 16.00100 number of atom coordinates read : 3056 total number of charged atoms : 2911 net assigned charge : 11.50002 assigned positive charge : 453.6618 centred at (gu) : 90.62712 91.07022 89.04604 assigned negative charge : -442.1631 centred at (gu) : 90.71485 91.08279 88.96224 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6137 nv = 96 ne = 84 npr = 59248 no. pairs analyzed = 59248 no. exposed pairs = 4240 no. arc points = 30886 no. surface atoms = 1423 nbur = 1633 mkacc time = 0.1300000 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 = 1.568000 m= 268 mr = 2862 m= 1 mr = 7 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 0.3100000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3169 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7925 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2436049E-10 1.0996011E-09 midg,1,midg; midg,igrid,midg 6.8290085E-10 9.0680696E-10 1,midg,midg; igrid,midg,midg 1.2136308E-09 1.7641710E-10 gauss-seidel spectral radius is 0.9828662 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 08:56:00 rms-change max change #iterations 7.1296841E-02 13.00486 at 10iterations 4.8224535E-03 0.8133888 at 20iterations 3.1969493E-04 5.9665680E-02 at 30iterations 2.3665787E-05 3.4828186E-03 at 40iterations 2.1293283E-06 3.0517578E-04 at 50iterations finished qdiffx linear iterations at : 08:56:03 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 2.1293283E-06 3.0517578E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 08:56:06 3.161u 0.135s 0:06.45 51.0% 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 Wed Feb 15 2012 at 08:56:06 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 = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.644671 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): 9.401000 71.95800 ymin,ymax (A): -1.397000 63.54000 zmin,zma (A): -5.290000 37.29200 x,y,z range (A): 62.55700 64.93700 42.58200 scale (grids/A): 1.644671 object centre (A): 40.67950 31.07150 16.00100 number of atom coordinates read : 3056 total number of charged atoms : 2911 net assigned charge : 11.50002 assigned positive charge : 453.6618 centred at (gu) : 91.88039 93.20970 87.13723 assigned negative charge : -442.1631 centred at (gu) : 92.14401 93.24783 86.88632 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30886 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19875 mr = 42202 m= 2066 mr = 13120 m= 61 mr = 900 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 489 time to turn everything in is 0.4700000 number of dielectric boundary points 32612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 382 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 22304 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) : 0.5482236 object centre at (A) : 40.67950 31.07150 16.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9954639E-03 5.8106766E-03 midg,1,midg; midg,igrid,midg -2.0278255E-03 -6.8053743E-03 1,midg,midg; igrid,midg,midg 2.6501231E-02 1.0529202E-02 gauss-seidel spectral radius is 0.9982303 estimated iterations to convergence 189 setup time was (sec) 0.7500000 now iterating at: 08:56:07 rms-change max change #iterations 3.346414 158.3500 at 10iterations 1.396769 57.13682 at 20iterations 0.5853760 22.62895 at 30iterations 0.2468722 10.56374 at 40iterations 0.1032779 3.833067 at 50iterations 4.3471090E-02 1.444518 at 60iterations 1.8235406E-02 0.6530628 at 70iterations 7.6541002E-03 0.2856131 at 80iterations 3.2228692E-03 0.1111994 at 90iterations 1.3599193E-03 5.1672220E-02 at 100iterations 5.7140499E-04 1.9927979E-02 at 110iterations 2.4029307E-04 8.9159012E-03 at 120iterations finished qdiffx linear iterations at : 08:56:14 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 2.4029307E-04 8.9159012E-03 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 08:56:14 7.475u 0.192s 0:07.99 95.8% 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 Wed Feb 15 2012 at 08:56:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.467006 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): 9.401000 71.95800 ymin,ymax (A): -1.397000 63.54000 zmin,zma (A): -5.290000 37.29200 x,y,z range (A): 62.55700 64.93700 42.58200 scale (grids/A): 2.467006 object centre (A): 40.67950 31.07150 16.00100 number of atom coordinates read : 3056 total number of charged atoms : 2911 net assigned charge : 11.50002 assigned positive charge : 453.6618 centred at (gu) : 92.82054 94.81431 85.70548 assigned negative charge : -442.1631 centred at (gu) : 93.21586 94.87173 85.32948 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 154870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30886 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68235 mr = 103954 m= 19308 mr = 52175 m= 2848 mr = 13962 m= 181 mr = 1721 m= 5 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1733 time to turn everything in is 1.080000 number of dielectric boundary points 73563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 23266 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) : 1.644671 object centre at (A) : 40.67950 31.07150 16.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1335879 6.8123221E-02 midg,1,midg; midg,igrid,midg -5.7675175E-02 -8.3271481E-02 1,midg,midg; igrid,midg,midg 0.3664319 0.1300569 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.350000 now iterating at: 08:56:16 rms-change max change #iterations 8.806600 325.9766 at 10iterations 5.018636 136.4872 at 20iterations 2.848287 62.54601 at 30iterations 1.603649 37.82667 at 40iterations 0.8967978 19.04462 at 50iterations 0.5009476 11.43397 at 60iterations 0.2791413 6.247017 at 70iterations 0.1552884 3.037903 at 80iterations 8.6428702E-02 1.805695 at 90iterations 4.7971394E-02 1.006660 at 100iterations 2.6566146E-02 0.5565221 at 110iterations 1.4711902E-02 0.3025703 at 120iterations 8.1547750E-03 0.1741498 at 130iterations 4.5063216E-03 9.6286774E-02 at 140iterations 2.4977070E-03 4.9863100E-02 at 150iterations 1.3799251E-03 2.9140472E-02 at 160iterations 7.6447491E-04 1.4836788E-02 at 170iterations 4.2230359E-04 8.4075928E-03 at 180iterations finished qdiffx linear iterations at : 08:56:25 total time elapsed so far: 10.84000 # loops : 180 mean,max change (kT/e) : 4.2230359E-04 8.4075928E-03 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 08:56:26 11.035u 0.187s 0:11.62 96.4% 0+0k 0+0io 0pf+0w