Sun Oct 9 07:21:53 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 07:21:53 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2496 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5434949 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): -4.243000 41.97600 ymin,ymax (A): 35.80600 87.32500 zmin,zma (A): -3.932000 61.57000 x,y,z range (A): 46.21900 51.51900 65.50200 scale (grids/A): 0.5434949 object centre (A): 18.86650 61.56550 28.81900 number of atom coordinates read : 2496 total number of charged atoms : 2351 net assigned charge : -10.49998 assigned positive charge : 374.5269 centred at (gu) : 90.61230 89.05447 89.65939 assigned negative charge : -385.0274 centred at (gu) : 90.77122 88.69070 89.57151 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4778 nv = 96 ne = 84 npr = 49971 no. pairs analyzed = 49971 no. exposed pairs = 3536 no. arc points = 25351 no. surface atoms = 1185 nbur = 1311 mkacc time = 0.1100000 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= 186 mr = 2172 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1142943E-09 -9.8735749E-11 midg,1,midg; midg,igrid,midg -3.2395180E-09 9.8723052E-10 1,midg,midg; igrid,midg,midg 2.1485004E-10 -1.6396474E-09 gauss-seidel spectral radius is 0.9825172 estimated iterations to convergence 62 setup time was (sec) 0.5400000 now iterating at: 07:21:54 rms-change max change #iterations 6.3156843E-02 13.77321 at 10iterations 3.9764270E-03 0.7951393 at 20iterations 2.6669572E-04 4.9608231E-02 at 30iterations 1.8095290E-05 3.3817291E-03 at 40iterations 1.3439935E-06 2.3651123E-04 at 50iterations finished qdiffx linear iterations at : 07:21:57 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.3439935E-06 2.3651123E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 07:21:57 3.561u 0.192s 0:04.03 93.0% 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 07:21:57 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2496 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: 1.630485 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): -4.243000 41.97600 ymin,ymax (A): 35.80600 87.32500 zmin,zma (A): -3.932000 61.57000 x,y,z range (A): 46.21900 51.51900 65.50200 scale (grids/A): 1.630485 object centre (A): 18.86650 61.56550 28.81900 number of atom coordinates read : 2496 total number of charged atoms : 2351 net assigned charge : -10.49998 assigned positive charge : 374.5269 centred at (gu) : 91.83657 87.16297 88.97749 assigned negative charge : -385.0274 centred at (gu) : 92.31333 86.07191 88.71418 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 52933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25351 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15182 mr = 33122 m= 1331 mr = 9863 m= 33 mr = 542 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.4400000 number of dielectric boundary points 25949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 17993 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) : 0.5434949 object centre at (A) : 18.86650 61.56550 28.81900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2848861E-02 5.9719444E-03 midg,1,midg; midg,igrid,midg -2.2740316E-02 6.8245414E-03 1,midg,midg; igrid,midg,midg -2.9712336E-03 -1.5373946E-02 gauss-seidel spectral radius is 0.9981273 estimated iterations to convergence 184 setup time was (sec) 0.7500000 now iterating at: 07:21:58 rms-change max change #iterations 3.002487 190.9165 at 10iterations 1.230883 52.90714 at 20iterations 0.5036490 21.49763 at 30iterations 0.2071567 7.563639 at 40iterations 8.4937312E-02 3.495934 at 50iterations 3.4883317E-02 1.488173 at 60iterations 1.4237237E-02 0.5791950 at 70iterations 5.8627268E-03 0.2276268 at 80iterations 2.4023124E-03 9.6839905E-02 at 90iterations 9.8828506E-04 3.7620544E-02 at 100iterations 4.0602437E-04 1.5914917E-02 at 110iterations 1.6699580E-04 6.6282749E-03 at 120iterations finished qdiffx linear iterations at : 07:22:05 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.6699580E-04 6.6282749E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 07:22:06 7.857u 0.206s 0:08.45 95.2% 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 07:22:06 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2496 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.445727 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): -4.243000 41.97600 ymin,ymax (A): 35.80600 87.32500 zmin,zma (A): -3.932000 61.57000 x,y,z range (A): 46.21900 51.51900 65.50200 scale (grids/A): 2.445727 object centre (A): 18.86650 61.56550 28.81900 number of atom coordinates read : 2496 total number of charged atoms : 2351 net assigned charge : -10.49998 assigned positive charge : 374.5269 centred at (gu) : 92.75476 85.74429 88.46621 assigned negative charge : -385.0274 centred at (gu) : 93.46995 84.10773 88.07119 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 122306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25351 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 53325 mr = 81358 m= 13725 mr = 40626 m= 1941 mr = 9725 m= 97 mr = 1135 m= 0 mr = 39 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 0.9900000 number of dielectric boundary points 58511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18789 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) : 1.630485 object centre at (A) : 18.86650 61.56550 28.81900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8226718 6.6926733E-02 midg,1,midg; midg,igrid,midg -0.3069283 9.8135114E-02 1,midg,midg; igrid,midg,midg -4.3980777E-02 -0.1970408 gauss-seidel spectral radius is 0.9991118 estimated iterations to convergence 265 setup time was (sec) 1.310000 now iterating at: 07:22:07 rms-change max change #iterations 7.897333 314.9951 at 10iterations 4.376777 117.4490 at 20iterations 2.429491 62.80401 at 30iterations 1.339772 37.90163 at 40iterations 0.7383519 18.84973 at 50iterations 0.4046184 10.29509 at 60iterations 0.2213297 5.446291 at 70iterations 0.1208928 2.891529 at 80iterations 6.6159509E-02 1.522902 at 90iterations 3.6107499E-02 0.8552094 at 100iterations 1.9670205E-02 0.4511111 at 110iterations 1.0736731E-02 0.2560425 at 120iterations 5.8478150E-03 0.1440897 at 130iterations 3.1904096E-03 7.3007584E-02 at 140iterations 1.7346384E-03 4.0456772E-02 at 150iterations 9.4450807E-04 2.4225235E-02 at 160iterations 5.1272172E-04 1.0931015E-02 at 170iterations 2.7961194E-04 7.8530312E-03 at 180iterations finished qdiffx linear iterations at : 07:22:18 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 2.7961194E-04 7.8530312E-03 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 07:22:19 12.411u 0.235s 0:12.92 97.8% 0+0k 0+0io 0pf+0w