Mon Oct 10 22:34:14 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 Mon Oct 10 2011 at 22:34:14 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 = 2630 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: 0.6722181 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): -19.60100 30.83100 ymin,ymax (A): 20.10200 73.06100 zmin,zma (A): 9.254001 51.86400 x,y,z range (A): 50.43200 52.95900 42.61000 scale (grids/A): 0.6722181 object centre (A): 5.615000 46.58150 30.55900 number of atom coordinates read : 2630 total number of charged atoms : 2489 net assigned charge : 6.500025 assigned positive charge : 394.9897 centred at (gu) : 91.48772 89.35078 89.84776 assigned negative charge : -388.4904 centred at (gu) : 91.48120 89.64335 90.06497 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7854 nv = 96 ne = 84 npr = 53952 no. pairs analyzed = 53952 no. exposed pairs = 3038 no. arc points = 21104 no. surface atoms = 1026 nbur = 1604 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4574 m= 0 mr = 69 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 179 time to turn everything in is 0.3300000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1857 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1900758E-08 -3.6211951E-08 midg,1,midg; midg,igrid,midg 1.1274746E-07 -5.1189176E-08 1,midg,midg; igrid,midg,midg 1.5394086E-08 3.2362550E-08 gauss-seidel spectral radius is 0.9885265 estimated iterations to convergence 76 setup time was (sec) 0.5800000 now iterating at: 22:34:15 rms-change max change #iterations 0.1842905 25.11448 at 10iterations 2.0925149E-02 2.789063 at 20iterations 2.8980032E-03 0.5381165 at 30iterations 6.5813481E-04 0.1349449 at 40iterations 2.2080679E-04 4.6466827E-02 at 50iterations finished qdiffx linear iterations at : 22:34:18 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.2080679E-04 4.6466827E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 22:34:18 3.572u 0.188s 0:04.34 86.4% 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 Mon Oct 10 2011 at 22:34:19 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 = 2630 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: 2.016654 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): -19.60100 30.83100 ymin,ymax (A): 20.10200 73.06100 zmin,zma (A): 9.254001 51.86400 x,y,z range (A): 50.43200 52.95900 42.61000 scale (grids/A): 2.016654 object centre (A): 5.615000 46.58150 30.55900 number of atom coordinates read : 2630 total number of charged atoms : 2489 net assigned charge : 6.500025 assigned positive charge : 394.9897 centred at (gu) : 94.46251 88.05158 89.54276 assigned negative charge : -388.4904 centred at (gu) : 94.44325 88.92960 90.19456 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 84741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21104 grid for indexing accessible points = 1.400000 m= 31814 mr = 60306 m= 5682 mr = 24364 m= 417 mr = 3957 m= 8 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4359 time to turn everything in is 0.6600000 number of dielectric boundary points 33808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19683 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) : 0.6722181 object centre at (A) : 5.615000 46.58150 30.55900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6478050E-02 3.7926235E-03 midg,1,midg; midg,igrid,midg 2.3149889E-02 -3.7273824E-02 1,midg,midg; igrid,midg,midg 1.9820275E-02 2.4262320E-03 gauss-seidel spectral radius is 0.9987713 estimated iterations to convergence 226 setup time was (sec) 0.9800000 now iterating at: 22:34:20 rms-change max change #iterations 4.741714 186.3031 at 10iterations 2.306599 74.77030 at 20iterations 1.124963 34.07397 at 30iterations 0.5470870 15.96783 at 40iterations 0.2670025 7.675629 at 50iterations 0.1304241 3.790416 at 60iterations 6.3536942E-02 1.845249 at 70iterations 3.1273790E-02 0.8700676 at 80iterations 1.5383523E-02 0.4355011 at 90iterations 7.6541314E-03 0.2220116 at 100iterations 3.8917016E-03 0.1324768 at 110iterations 2.0652330E-03 7.0709229E-02 at 120iterations finished qdiffx linear iterations at : 22:34:27 total time elapsed so far: 8.580000 # loops : 120 mean,max change (kT/e) : 2.0652330E-03 7.0709229E-02 energy calculations done at 8.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.770000 DelPhi exited at 22:34:28 8.774u 0.197s 0:09.26 96.7% 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 Mon Oct 10 2011 at 22:34:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2630 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: 3.024981 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): -19.60100 30.83100 ymin,ymax (A): 20.10200 73.06100 zmin,zma (A): 9.254001 51.86400 x,y,z range (A): 50.43200 52.95900 42.61000 scale (grids/A): 3.024981 object centre (A): 5.615000 46.58150 30.55900 number of atom coordinates read : 2630 total number of charged atoms : 2489 net assigned charge : 6.500025 assigned positive charge : 394.9897 centred at (gu) : 96.69354 87.07717 89.31408 assigned negative charge : -388.4904 centred at (gu) : 96.66488 88.39437 90.29174 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 195885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21104 grid for indexing accessible points = 1.400000 m= 101496 mr = 145376 m= 39049 mr = 84712 m= 10512 mr = 32528 m= 1882 mr = 8514 m= 197 mr = 1428 m= 7 mr = 139 m= 0 mr = 5 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 14566 time to turn everything in is 1.610000 number of dielectric boundary points 76326 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 19912 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) : 2.016654 object centre at (A) : 5.615000 46.58150 30.55900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4881652 0.1064054 midg,1,midg; midg,igrid,midg -0.2404321 -0.3054430 1,midg,midg; igrid,midg,midg 0.1160544 6.3916117E-02 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 1.940000 now iterating at: 22:34:30 rms-change max change #iterations 10.75062 396.8088 at 10iterations 6.285500 140.6012 at 20iterations 3.671069 71.83385 at 30iterations 2.143176 36.77632 at 40iterations 1.248104 22.47523 at 50iterations 0.7261463 12.72621 at 60iterations 0.4227364 7.035110 at 70iterations 0.2459328 4.161739 at 80iterations 0.1428529 2.744390 at 90iterations 8.3320245E-02 1.412563 at 100iterations 4.8499059E-02 0.8922901 at 110iterations 2.8262423E-02 0.5173264 at 120iterations 1.6534941E-02 0.2938118 at 130iterations 9.7795082E-03 0.1706696 at 140iterations 5.8482490E-03 0.1155357 at 150iterations 3.5971617E-03 7.2975159E-02 at 160iterations 2.3174756E-03 5.0609589E-02 at 170iterations 1.5847811E-03 3.8963318E-02 at 180iterations finished qdiffx linear iterations at : 22:34:41 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 1.5847811E-03 3.8963318E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 22:34:42 13.234u 0.261s 0:14.17 95.2% 0+0k 0+0io 0pf+0w