Tue Oct 11 03:48:06 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 03:48:07 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6427617 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): -46.19200 1.169000 ymin,ymax (A): -47.35200 1.721000 zmin,zma (A): -9.718000 45.66800 x,y,z range (A): 47.36100 49.07300 55.38600 scale (grids/A): 0.6427617 object centre (A): -22.51150 -22.81550 17.97500 number of atom coordinates read : 2741 total number of charged atoms : 2589 net assigned charge : 4.154017 assigned positive charge : 416.5858 centred at (gu) : 89.89294 90.44821 91.83923 assigned negative charge : -412.4323 centred at (gu) : 89.61377 90.23669 91.80462 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7564 nv = 96 ne = 84 npr = 56322 no. pairs analyzed = 56322 no. exposed pairs = 3256 no. arc points = 22731 no. surface atoms = 1095 nbur = 1646 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4333 m= 4 mr = 66 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 0.3400000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2247 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9073 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3037451E-09 1.6286670E-08 midg,1,midg; midg,igrid,midg -2.0290233E-08 3.7387323E-08 1,midg,midg; igrid,midg,midg -3.2662868E-08 4.1516564E-08 gauss-seidel spectral radius is 0.9874675 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 03:48:07 rms-change max change #iterations 0.1545715 23.94072 at 10iterations 1.5809353E-02 2.106731 at 20iterations 1.5863772E-03 0.2374878 at 30iterations 1.7514569E-04 2.1714211E-02 at 40iterations 2.7865337E-05 4.4403076E-03 at 50iterations finished qdiffx linear iterations at : 03:48:10 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 2.7865337E-05 4.4403076E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 03:48:11 3.578u 0.190s 0:04.16 90.3% 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 03:48:11 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.928285 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): -46.19200 1.169000 ymin,ymax (A): -47.35200 1.721000 zmin,zma (A): -9.718000 45.66800 x,y,z range (A): 47.36100 49.07300 55.38600 scale (grids/A): 1.928285 object centre (A): -22.51150 -22.81550 17.97500 number of atom coordinates read : 2741 total number of charged atoms : 2589 net assigned charge : 4.154017 assigned positive charge : 416.5858 centred at (gu) : 89.67829 91.34431 95.51701 assigned negative charge : -412.4323 centred at (gu) : 88.84102 90.70959 95.41364 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81730 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22731 grid for indexing accessible points = 1.400000 m= 31036 mr = 58298 m= 5102 mr = 23453 m= 290 mr = 3258 m= 2 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 973 time to turn everything in is 0.6300000 number of dielectric boundary points 33054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20373 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) : 0.6427617 object centre at (A) : -22.51150 -22.81550 17.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0842463E-02 1.3318955E-02 midg,1,midg; midg,igrid,midg -1.3293359E-02 3.9899364E-02 1,midg,midg; igrid,midg,midg -1.5857454E-02 5.3937376E-02 gauss-seidel spectral radius is 0.9986792 estimated iterations to convergence 218 setup time was (sec) 0.9400000 now iterating at: 03:48:12 rms-change max change #iterations 4.491576 186.1536 at 10iterations 2.133633 69.45860 at 20iterations 1.016922 31.74677 at 30iterations 0.4842839 14.33454 at 40iterations 0.2295647 7.899492 at 50iterations 0.1089069 3.163729 at 60iterations 5.1883526E-02 1.534840 at 70iterations 2.4634851E-02 0.6923532 at 80iterations 1.1695744E-02 0.3663626 at 90iterations 5.5441908E-03 0.1768684 at 100iterations 2.6326324E-03 7.7417195E-02 at 110iterations 1.2570894E-03 3.8497925E-02 at 120iterations finished qdiffx linear iterations at : 03:48:19 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.2570894E-03 3.8497925E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 03:48:20 8.092u 0.233s 0:08.85 94.0% 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 Tue Oct 11 2011 at 03:48:20 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.892428 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): -46.19200 1.169000 ymin,ymax (A): -47.35200 1.721000 zmin,zma (A): -9.718000 45.66800 x,y,z range (A): 47.36100 49.07300 55.38600 scale (grids/A): 2.892428 object centre (A): -22.51150 -22.81550 17.97500 number of atom coordinates read : 2741 total number of charged atoms : 2589 net assigned charge : 4.154017 assigned positive charge : 416.5858 centred at (gu) : 89.51723 92.01643 98.27547 assigned negative charge : -412.4323 centred at (gu) : 88.26157 91.06433 98.12028 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 189205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22731 grid for indexing accessible points = 1.400000 m= 100051 mr = 140954 m= 37044 mr = 83234 m= 9157 mr = 30239 m= 1299 mr = 6900 m= 76 mr = 890 m= 0 mr = 20 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 3253 time to turn everything in is 1.610000 number of dielectric boundary points 74595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 20703 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) : 1.928285 object centre at (A) : -22.51150 -22.81550 17.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3042342 0.4137517 midg,1,midg; midg,igrid,midg -0.1690263 0.4443693 1,midg,midg; igrid,midg,midg -0.1247476 0.4355242 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 1.940000 now iterating at: 03:48:22 rms-change max change #iterations 10.49323 353.4695 at 10iterations 6.146632 129.8080 at 20iterations 3.574940 76.88597 at 30iterations 2.087100 46.38536 at 40iterations 1.210140 24.86816 at 50iterations 0.7022256 12.77127 at 60iterations 0.4056154 7.529593 at 70iterations 0.2348946 4.316313 at 80iterations 0.1357723 2.360529 at 90iterations 7.8678936E-02 1.385750 at 100iterations 4.5335047E-02 0.7997875 at 110iterations 2.6156139E-02 0.4624472 at 120iterations 1.5107734E-02 0.2665100 at 130iterations 8.7305186E-03 0.1495209 at 140iterations 5.0403900E-03 8.1853867E-02 at 150iterations 2.8989732E-03 4.9884796E-02 at 160iterations 1.6728850E-03 2.8604507E-02 at 170iterations 9.6598396E-04 1.6895294E-02 at 180iterations finished qdiffx linear iterations at : 03:48:33 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 9.6598396E-04 1.6895294E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 03:48:34 13.173u 0.246s 0:13.85 96.8% 0+0k 0+0io 0pf+0w