Tue Oct 11 04:26:29 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 04:26:29 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 !!! WARNING: HIR 43 has a net charge of 0.5140 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: 0.6579555 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): -10.78800 37.20800 ymin,ymax (A): -26.20800 22.27400 zmin,zma (A): -8.349000 45.75800 x,y,z range (A): 47.99600 48.48200 54.10700 scale (grids/A): 0.6579555 object centre (A): 13.21000 -1.967000 18.70450 number of atom coordinates read : 2706 total number of charged atoms : 2558 net assigned charge : 2.514024 assigned positive charge : 411.7796 centred at (gu) : 90.01472 90.38676 91.25455 assigned negative charge : -409.2663 centred at (gu) : 89.78323 90.24451 91.26888 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7857 nv = 96 ne = 84 npr = 55192 no. pairs analyzed = 55192 no. exposed pairs = 3307 no. arc points = 23022 no. surface atoms = 1111 nbur = 1595 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4501 m= 0 mr = 50 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3300000 number of dielectric boundary points 3770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2201 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9311 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8605792E-09 4.0611430E-09 midg,1,midg; midg,igrid,midg -2.0722553E-08 3.6602490E-08 1,midg,midg; igrid,midg,midg -4.0757396E-08 5.0843244E-08 gauss-seidel spectral radius is 0.9880356 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 04:26:30 rms-change max change #iterations 0.1705445 20.70947 at 10iterations 1.8244321E-02 2.447845 at 20iterations 2.0489611E-03 0.2630424 at 30iterations 2.6377867E-04 3.4906387E-02 at 40iterations 4.9165614E-05 7.1754456E-03 at 50iterations finished qdiffx linear iterations at : 04:26:33 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.9165614E-05 7.1754456E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 04:26:33 3.422u 0.158s 0:04.01 89.0% 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 04:26:33 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 !!! WARNING: HIR 43 has a net charge of 0.5140 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: 1.973867 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): -10.78800 37.20800 ymin,ymax (A): -26.20800 22.27400 zmin,zma (A): -8.349000 45.75800 x,y,z range (A): 47.99600 48.48200 54.10700 scale (grids/A): 1.973867 object centre (A): 13.21000 -1.967000 18.70450 number of atom coordinates read : 2706 total number of charged atoms : 2558 net assigned charge : 2.514024 assigned positive charge : 411.7796 centred at (gu) : 90.04369 91.15963 93.76325 assigned negative charge : -409.2663 centred at (gu) : 89.34940 90.73327 93.80627 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 31970 mr = 60536 m= 5273 mr = 23892 m= 332 mr = 3298 m= 4 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.6200000 number of dielectric boundary points 34963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20211 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) : 0.6579555 object centre at (A) : 13.21000 -1.967000 18.70450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0674359E-02 -1.1526071E-02 midg,1,midg; midg,igrid,midg -1.2095840E-02 2.8184138E-02 1,midg,midg; igrid,midg,midg -1.4919435E-02 6.6250712E-02 gauss-seidel spectral radius is 0.9987381 estimated iterations to convergence 223 setup time was (sec) 0.9100000 now iterating at: 04:26:34 rms-change max change #iterations 4.692038 214.3441 at 10iterations 2.266450 71.19885 at 20iterations 1.094603 35.31059 at 30iterations 0.5276954 16.68783 at 40iterations 0.2556369 8.671392 at 50iterations 0.1233987 3.418594 at 60iterations 5.9708286E-02 1.758623 at 70iterations 2.8777745E-02 0.8511791 at 80iterations 1.3931816E-02 0.3850937 at 90iterations 6.7406003E-03 0.1864467 at 100iterations 3.2798343E-03 0.1049194 at 110iterations 1.5974542E-03 4.8378944E-02 at 120iterations finished qdiffx linear iterations at : 04:26:41 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.5974542E-03 4.8378944E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 04:26:42 7.759u 0.213s 0:08.46 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 04:26:42 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 !!! WARNING: HIR 43 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.960800 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): -10.78800 37.20800 ymin,ymax (A): -26.20800 22.27400 zmin,zma (A): -8.349000 45.75800 x,y,z range (A): 47.99600 48.48200 54.10700 scale (grids/A): 2.960800 object centre (A): 13.21000 -1.967000 18.70450 number of atom coordinates read : 2706 total number of charged atoms : 2558 net assigned charge : 2.514024 assigned positive charge : 411.7796 centred at (gu) : 90.06535 91.73924 95.64469 assigned negative charge : -409.2663 centred at (gu) : 89.02410 91.09987 95.70937 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 196946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 102620 mr = 145892 m= 38104 mr = 85032 m= 9383 mr = 30809 m= 1427 mr = 7018 m= 87 mr = 952 m= 0 mr = 41 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1422 time to turn everything in is 1.630000 number of dielectric boundary points 78823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 20464 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) : 1.973867 object centre at (A) : 13.21000 -1.967000 18.70450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5849895 0.1722432 midg,1,midg; midg,igrid,midg -0.1370395 0.3507349 1,midg,midg; igrid,midg,midg -9.9498741E-02 0.5644315 gauss-seidel spectral radius is 0.9992820 estimated iterations to convergence 294 setup time was (sec) 1.930000 now iterating at: 04:26:44 rms-change max change #iterations 10.81142 404.6478 at 10iterations 6.344718 129.3597 at 20iterations 3.718713 75.15681 at 30iterations 2.169979 40.19389 at 40iterations 1.268745 23.34811 at 50iterations 0.7414031 13.19328 at 60iterations 0.4320009 8.059395 at 70iterations 0.2511488 4.221317 at 80iterations 0.1461270 2.524380 at 90iterations 8.4976166E-02 1.448277 at 100iterations 4.9499240E-02 0.8103752 at 110iterations 2.8861098E-02 0.5145210 at 120iterations 1.6784836E-02 0.2761304 at 130iterations 9.8073399E-03 0.1718683 at 140iterations 5.7432381E-03 0.1014252 at 150iterations 3.3844262E-03 6.1927795E-02 at 160iterations 2.0197432E-03 3.7975311E-02 at 170iterations 1.2275799E-03 2.5043488E-02 at 180iterations finished qdiffx linear iterations at : 04:26:55 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.2275799E-03 2.5043488E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 04:26:55 13.097u 0.226s 0:13.68 97.2% 0+0k 0+0io 0pf+0w