Mon Oct 10 14:00:38 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 Mon Oct 10 2011 at 14:00:38 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: GLM 201 has a net charge of -0.0940 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: 0.6038606 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 0.6038606 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 2018 total number of charged atoms : 1862 net assigned charge : 1.906005 assigned positive charge : 295.4470 centred at (gu) : 90.07020 90.05165 90.30550 assigned negative charge : -293.5413 centred at (gu) : 90.10125 90.12270 90.43996 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4944 nv = 96 ne = 84 npr = 40776 no. pairs analyzed = 40776 no. exposed pairs = 2554 no. arc points = 17558 no. surface atoms = 883 nbur = 1135 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 254 mr = 2678 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1798 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 5979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7243578E-09 -3.5456751E-09 midg,1,midg; midg,igrid,midg 3.1014888E-09 -1.2977057E-09 1,midg,midg; igrid,midg,midg 1.8786659E-09 -2.4222445E-11 gauss-seidel spectral radius is 0.9857566 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 14:00:39 rms-change max change #iterations 0.1018304 19.99676 at 10iterations 8.5821236E-03 1.473387 at 20iterations 7.3276396E-04 0.1297798 at 30iterations 6.4162770E-05 1.0227203E-02 at 40iterations 5.4712227E-06 8.1443787E-04 at 50iterations finished qdiffx linear iterations at : 14:00:43 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 5.4712227E-06 8.1443787E-04 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 14:00:44 4.646u 0.382s 0:06.21 80.8% 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 14:00:44 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: GLM 201 has a net charge of -0.0940 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: 1.811582 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 1.811582 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 2018 total number of charged atoms : 1862 net assigned charge : 1.906005 assigned positive charge : 295.4470 centred at (gu) : 90.21072 90.15496 90.91635 assigned negative charge : -293.5413 centred at (gu) : 90.30396 90.36830 91.32012 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 52924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 19394 mr = 36043 m= 2862 mr = 14547 m= 135 mr = 1801 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 22885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14541 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) : 0.6038606 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7891511E-03 -8.1467573E-03 midg,1,midg; midg,igrid,midg 9.4301801E-04 -3.3260456E-03 1,midg,midg; igrid,midg,midg 4.2637806E-02 2.9842602E-02 gauss-seidel spectral radius is 0.9984244 estimated iterations to convergence 200 setup time was (sec) 0.8700000 now iterating at: 14:00:45 rms-change max change #iterations 3.300503 149.1242 at 10iterations 1.455484 56.91074 at 20iterations 0.6455484 25.59372 at 30iterations 0.2848177 11.72339 at 40iterations 0.1257773 5.282436 at 50iterations 5.5602171E-02 2.398375 at 60iterations 2.4704956E-02 0.8521452 at 70iterations 1.0889603E-02 0.4313993 at 80iterations 4.8320377E-03 0.1861954 at 90iterations 2.1303773E-03 8.2879066E-02 at 100iterations 9.4690517E-04 3.2604218E-02 at 110iterations 4.1900543E-04 1.7036438E-02 at 120iterations finished qdiffx linear iterations at : 14:00:55 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 4.1900543E-04 1.7036438E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 14:00:56 10.589u 0.345s 0:11.32 96.4% 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 14:00:56 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: GLM 201 has a net charge of -0.0940 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: 2.717373 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 2.717373 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 2018 total number of charged atoms : 1862 net assigned charge : 1.906005 assigned positive charge : 295.4470 centred at (gu) : 90.31609 90.23243 91.37454 assigned negative charge : -293.5413 centred at (gu) : 90.45605 90.55248 91.98026 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 122172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 61945 mr = 87086 m= 22730 mr = 50945 m= 5155 mr = 18580 m= 602 mr = 3959 m= 31 mr = 407 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 51655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14890 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) : 1.811582 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7991229E-02 -7.3087394E-02 midg,1,midg; midg,igrid,midg -1.9109836E-02 -2.9698672E-02 1,midg,midg; igrid,midg,midg 0.4711305 0.3527768 gauss-seidel spectral radius is 0.9991832 estimated iterations to convergence 276 setup time was (sec) 1.580000 now iterating at: 14:00:57 rms-change max change #iterations 8.032721 343.0854 at 10iterations 4.590055 134.6733 at 20iterations 2.591150 59.78729 at 30iterations 1.462878 33.46886 at 40iterations 0.8194175 20.77496 at 50iterations 0.4596485 11.54388 at 60iterations 0.2572209 5.413727 at 70iterations 0.1439367 2.997292 at 80iterations 8.0536887E-02 1.671218 at 90iterations 4.5140669E-02 1.021940 at 100iterations 2.5182376E-02 0.5370426 at 110iterations 1.4066456E-02 0.2975245 at 120iterations 7.8386078E-03 0.1697755 at 130iterations 4.3735588E-03 9.1970205E-02 at 140iterations 2.4441925E-03 5.0807953E-02 at 150iterations 1.3644883E-03 3.2123566E-02 at 160iterations 7.6096744E-04 1.7326355E-02 at 170iterations 4.2471432E-04 8.7738037E-03 at 180iterations finished qdiffx linear iterations at : 14:01:12 total time elapsed so far: 15.70000 # loops : 180 mean,max change (kT/e) : 4.2471432E-04 8.7738037E-03 energy calculations done at 15.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.88000 DelPhi exited at 14:01:13 15.878u 0.423s 0:17.19 94.7% 0+0k 0+0io 0pf+0w