Sun Oct 9 09:57:05 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 Sun Oct 9 2011 at 09:57:05 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: HIR 219 has a net charge of 0.5140 !!! WARNING: ASP 494 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6029096 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): -14.01700 40.03200 ymin,ymax (A): -25.48600 33.56100 zmin,zma (A): -2.162000 48.78500 x,y,z range (A): 54.04900 59.04700 50.94700 scale (grids/A): 0.6029096 object centre (A): 13.00750 4.037500 23.31150 number of atom coordinates read : 2837 total number of charged atoms : 2721 net assigned charge : 1.014016 assigned positive charge : 419.1972 centred at (gu) : 89.85625 89.89995 90.71100 assigned negative charge : -418.1848 centred at (gu) : 89.73970 89.97230 90.68791 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7042 nv = 96 ne = 84 npr = 56187 no. pairs analyzed = 56187 no. exposed pairs = 3868 no. arc points = 26823 no. surface atoms = 1286 nbur = 1551 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3602 m= 3 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 0.2200000 number of dielectric boundary points 3803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2729 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3656051E-10 1.7262246E-09 midg,1,midg; midg,igrid,midg 3.6470080E-09 -2.5992655E-09 1,midg,midg; igrid,midg,midg -4.7598685E-09 5.2494666E-09 gauss-seidel spectral radius is 0.9857925 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 09:57:06 rms-change max change #iterations 0.1137816 18.22432 at 10iterations 9.7543458E-03 1.512527 at 20iterations 9.0813165E-04 0.1343536 at 30iterations 1.0887242E-04 1.5842438E-02 at 40iterations 1.9430039E-05 3.3950806E-03 at 50iterations finished qdiffx linear iterations at : 09:57:08 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.9430039E-05 3.3950806E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 09:57:09 3.395u 0.161s 0:03.82 92.9% 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 Sun Oct 9 2011 at 09:57:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: HIR 219 has a net charge of 0.5140 !!! WARNING: ASP 494 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.808729 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): -14.01700 40.03200 ymin,ymax (A): -25.48600 33.56100 zmin,zma (A): -2.162000 48.78500 x,y,z range (A): 54.04900 59.04700 50.94700 scale (grids/A): 1.808729 object centre (A): 13.00750 4.037500 23.31150 number of atom coordinates read : 2837 total number of charged atoms : 2721 net assigned charge : 1.014016 assigned positive charge : 419.1972 centred at (gu) : 89.56810 89.69884 92.13208 assigned negative charge : -418.1848 centred at (gu) : 89.21899 89.91673 92.06387 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26823 grid for indexing accessible points = 1.400000 m= 26902 mr = 51522 m= 4220 mr = 18644 m= 227 mr = 2414 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.3900000 number of dielectric boundary points 35160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 21310 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) : 0.6029096 object centre at (A) : 13.00750 4.037500 23.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1900811E-03 3.3140935E-03 midg,1,midg; midg,igrid,midg -1.0878886E-02 -2.9253278E-02 1,midg,midg; igrid,midg,midg -9.1076940E-03 2.1346757E-02 gauss-seidel spectral radius is 0.9985371 estimated iterations to convergence 207 setup time was (sec) 0.6000000 now iterating at: 09:57:10 rms-change max change #iterations 3.990745 171.6973 at 10iterations 1.816172 65.90577 at 20iterations 0.8271384 27.73365 at 30iterations 0.3766542 13.07410 at 40iterations 0.1718004 5.591095 at 50iterations 7.7928349E-02 2.436921 at 60iterations 3.5599615E-02 1.201592 at 70iterations 1.6274359E-02 0.5411091 at 80iterations 7.4303756E-03 0.2613001 at 90iterations 3.3971588E-03 0.1246605 at 100iterations 1.5582034E-03 5.3686142E-02 at 110iterations 7.1547757E-04 2.1698952E-02 at 120iterations finished qdiffx linear iterations at : 09:57:17 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 7.1547757E-04 2.1698952E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 09:57:17 7.777u 0.202s 0:08.30 96.0% 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 Sun Oct 9 2011 at 09:57:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: HIR 219 has a net charge of 0.5140 !!! WARNING: ASP 494 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.713093 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): -14.01700 40.03200 ymin,ymax (A): -25.48600 33.56100 zmin,zma (A): -2.162000 48.78500 x,y,z range (A): 54.04900 59.04700 50.94700 scale (grids/A): 2.713093 object centre (A): 13.00750 4.037500 23.31150 number of atom coordinates read : 2837 total number of charged atoms : 2721 net assigned charge : 1.014016 assigned positive charge : 419.1972 centred at (gu) : 89.35191 89.54806 93.19781 assigned negative charge : -418.1848 centred at (gu) : 88.82849 89.87504 93.09577 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 176973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26823 grid for indexing accessible points = 1.400000 m= 86923 mr = 125987 m= 31005 mr = 68475 m= 7463 mr = 23698 m= 950 mr = 5235 m= 34 mr = 561 m= 0 mr = 2 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1159 time to turn everything in is 0.9700000 number of dielectric boundary points 79390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 21763 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) : 1.808729 object centre at (A) : 13.00750 4.037500 23.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6695637E-02 1.8997394E-02 midg,1,midg; midg,igrid,midg -0.1218491 -0.9896150 1,midg,midg; igrid,midg,midg -8.9075036E-02 0.2920984 gauss-seidel spectral radius is 0.9992504 estimated iterations to convergence 288 setup time was (sec) 1.210000 now iterating at: 09:57:19 rms-change max change #iterations 9.906153 333.2998 at 10iterations 5.892961 179.5614 at 20iterations 3.459404 91.46176 at 30iterations 2.021807 44.42427 at 40iterations 1.175013 26.42738 at 50iterations 0.6823197 16.24727 at 60iterations 0.3937440 8.651241 at 70iterations 0.2270997 4.424486 at 80iterations 0.1307743 2.804611 at 90iterations 7.5305074E-02 1.629539 at 100iterations 4.3298528E-02 0.8991508 at 110iterations 2.4854003E-02 0.4751320 at 120iterations 1.4285469E-02 0.2666607 at 130iterations 8.1966203E-03 0.1557770 at 140iterations 4.7091907E-03 9.0726279E-02 at 150iterations 2.6978413E-03 5.9261322E-02 at 160iterations 1.5544061E-03 2.7023792E-02 at 170iterations 8.9573365E-04 1.6703129E-02 at 180iterations finished qdiffx linear iterations at : 09:57:30 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 8.9573365E-04 1.6703129E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 09:57:30 12.643u 0.199s 0:13.10 97.9% 0+0k 0+0io 0pf+0w