Sun Oct 9 16:03:43 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 16:03:43 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6349320 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): -15.53100 37.54000 ymin,ymax (A): 55.09700 108.4050 zmin,zma (A): -5.196000 50.87300 x,y,z range (A): 53.07100 53.30800 56.06900 scale (grids/A): 0.6349320 object centre (A): 11.00450 81.75100 22.83850 number of atom coordinates read : 3056 total number of charged atoms : 2904 net assigned charge : -4.687975 assigned positive charge : 449.7592 centred at (gu) : 90.16504 88.68366 91.39607 assigned negative charge : -454.4485 centred at (gu) : 90.20277 88.54666 91.43018 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8133 nv = 96 ne = 84 npr = 63344 no. pairs analyzed = 63344 no. exposed pairs = 3713 no. arc points = 25772 no. surface atoms = 1261 nbur = 1795 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 4464 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2570 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10006 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1973980E-09 -1.2948225E-08 midg,1,midg; midg,igrid,midg -2.9342383E-08 7.7555127E-09 1,midg,midg; igrid,midg,midg -1.0730610E-09 -1.0390092E-08 gauss-seidel spectral radius is 0.9871889 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 16:03:44 rms-change max change #iterations 0.1565016 29.78607 at 10iterations 1.5163578E-02 2.152241 at 20iterations 1.5275613E-03 0.2100138 at 30iterations 1.6549086E-04 2.1743774E-02 at 40iterations 2.3970311E-05 3.2136440E-03 at 50iterations finished qdiffx linear iterations at : 16:03:47 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 2.3970311E-05 3.2136440E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 16:03:47 3.204u 0.181s 0:03.75 90.1% 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 16:03:47 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.904796 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): -15.53100 37.54000 ymin,ymax (A): 55.09700 108.4050 zmin,zma (A): -5.196000 50.87300 x,y,z range (A): 53.07100 53.30800 56.06900 scale (grids/A): 1.904796 object centre (A): 11.00450 81.75100 22.83850 number of atom coordinates read : 3056 total number of charged atoms : 2904 net assigned charge : -4.687975 assigned positive charge : 449.7592 centred at (gu) : 90.49415 86.05007 94.18748 assigned negative charge : -454.4485 centred at (gu) : 90.60849 85.63991 94.29034 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25772 grid for indexing accessible points = 1.400000 m= 32174 mr = 61887 m= 5633 mr = 23380 m= 372 mr = 3539 m= 5 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 0.6000000 number of dielectric boundary points 37481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22908 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) : 0.6349320 object centre at (A) : 11.00450 81.75100 22.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8661419E-02 1.2228436E-02 midg,1,midg; midg,igrid,midg -3.4520220E-02 -8.5065253E-03 1,midg,midg; igrid,midg,midg -4.0500008E-02 -3.2949727E-02 gauss-seidel spectral radius is 0.9986739 estimated iterations to convergence 218 setup time was (sec) 0.8800000 now iterating at: 16:03:48 rms-change max change #iterations 4.599939 165.4207 at 10iterations 2.176089 74.89787 at 20iterations 1.028968 32.66931 at 30iterations 0.4862373 14.14273 at 40iterations 0.2298087 6.910709 at 50iterations 0.1088731 3.046028 at 60iterations 5.1328488E-02 1.525970 at 70iterations 2.4346745E-02 0.6900177 at 80iterations 1.1549541E-02 0.3302178 at 90iterations 5.4803044E-03 0.1726379 at 100iterations 2.5888411E-03 7.2202682E-02 at 110iterations 1.2297756E-03 3.6026001E-02 at 120iterations finished qdiffx linear iterations at : 16:03:54 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 1.2297756E-03 3.6026001E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 16:03:55 7.251u 0.211s 0:07.75 96.2% 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 16:03:55 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.857194 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): -15.53100 37.54000 ymin,ymax (A): 55.09700 108.4050 zmin,zma (A): -5.196000 50.87300 x,y,z range (A): 53.07100 53.30800 56.06900 scale (grids/A): 2.857194 object centre (A): 11.00450 81.75100 22.83850 number of atom coordinates read : 3056 total number of charged atoms : 2904 net assigned charge : -4.687975 assigned positive charge : 449.7592 centred at (gu) : 90.74098 84.07482 96.28099 assigned negative charge : -454.4485 centred at (gu) : 90.91261 83.46000 96.43555 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 204569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25772 grid for indexing accessible points = 1.400000 m= 102765 mr = 150287 m= 38928 mr = 83382 m= 10021 mr = 31024 m= 1477 mr = 7457 m= 93 mr = 1015 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1531 time to turn everything in is 1.560000 number of dielectric boundary points 84650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 23231 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) : 1.904796 object centre at (A) : 11.00450 81.75100 22.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3662602 0.2516522 midg,1,midg; midg,igrid,midg -0.3638860 -0.2499374 1,midg,midg; igrid,midg,midg -0.5122642 -0.3619200 gauss-seidel spectral radius is 0.9992781 estimated iterations to convergence 294 setup time was (sec) 1.850000 now iterating at: 16:03:57 rms-change max change #iterations 10.92145 433.3275 at 10iterations 6.443908 136.5457 at 20iterations 3.774239 74.29459 at 30iterations 2.212641 41.28043 at 40iterations 1.291633 23.76579 at 50iterations 0.7522622 15.15500 at 60iterations 0.4375325 7.938592 at 70iterations 0.2546704 4.510310 at 80iterations 0.1474797 2.684329 at 90iterations 8.5861444E-02 1.596508 at 100iterations 4.9733512E-02 0.8482857 at 110iterations 2.8902909E-02 0.5039949 at 120iterations 1.6762579E-02 0.2783742 at 130iterations 9.7117927E-03 0.1873097 at 140iterations 5.6354040E-03 9.4512939E-02 at 150iterations 3.2768757E-03 6.2314987E-02 at 160iterations 1.9033253E-03 3.3348083E-02 at 170iterations 1.1090371E-03 1.9568443E-02 at 180iterations finished qdiffx linear iterations at : 16:04:07 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 1.1090371E-03 1.9568443E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 16:04:07 11.795u 0.200s 0:12.28 97.6% 0+0k 0+0io 0pf+0w